When clearing cache, omega theme settings are deleted (or reloaded from .info file)

No, that should not happen... If I am understanding you correctly you are saying that the database stored setting ms get reverted to the .info file version on a cache clear? Can anyone else confirm this? Does this happen with the latest dev version? I am working with that version currently and did not experience that behavior.

Okay. I have tested this multiple times and with different setups now and really can't reproduce this. If you run across this problem again or have any further information on this (maybe also how to reproduce it) feel free to re-open this!

I am not sure whether it is a related one. But when I am clearing the cache I am losing the default layout / regions.

@vinoth.3v I'm assuming by layouts you are talking about Omega layouts? Are you using the 7.x-4.x-dev as the issue details suggest? If so, have you done a git pull so you have the latest version? Are you using a custom layout?

I've been unable to reproduce this on the latest 7.x-4.x-dev version, if you can give me some more details I'll take another look.

Omega custom layout, omega latest git, yes to all questions :)

some time, after clearing the cache, I am getting just the content area without my custom regions! But it works if I clear the cache again.

I still can't reproduce it either. Unless you got a step by step tutorial that brings me to a scenario that triggers this bug I don't think I'll be able to fix it. I have currently no clue where this bug (if it exists) would come from. Sounds kinda random... Maybe we can start with a list of modules that you have on your site?

drush pm-list --type=module --status=enabled

Paste that list here :)

Same problem here with a sub-sub domain setup. This could be very well be a problem because of my setup but thought I would mentioning it anyway. Didn't experienced this during 70% of the project but when placing some views generated blocks to postcript zones things got reset because of drush cc all

I exported (reverted) theme settings, deleted the vars manually from the variables table but drush cc all keeps resetting stuff.

This could be very well because of my particular setup and modules that I'm using so here's my list of currently enabled modules.

Package           Naam                                                       Versie               
 Administration    Administration menu (admin_menu)                           7.x-3.0-rc4          
 Administration    Administration menu Toolbar style (admin_menu_toolbar)     7.x-3.0-rc4          
 Chaos tool suite  Chaos tools (ctools)                                       7.x-1.2              
 Context           Context (context)                                          7.x-3.0-beta6        
 Context           Context layouts (context_layouts)                          7.x-3.0-beta6        
 Context           Context UI (context_ui)                                    7.x-3.0-beta6        
 Core              Block (block)                                              7.21                 
 Core              Database logging (dblog)                                   7.21                 
 Core              Field (field)                                              7.21                 
 Core              Field SQL storage (field_sql_storage)                      7.21                 
 Core              Field UI (field_ui)                                        7.21                 
 Core              File (file)                                                7.21                 
 Core              Filter (filter)                                            7.21                 
 Core              Image (image)                                              7.21                 
 Core              List (list)                                                7.21                 
 Core              Locale (locale)                                            7.21                 
 Core              Menu (menu)                                                7.21                 
 Core              Node (node)                                                7.21                 
 Core              Options (options)                                          7.21                 
 Core              System (system)                                            7.21                 
 Core              Taxonomy (taxonomy)                                        7.21                 
 Core              Text (text)                                                7.21                 
 Core              Update manager (update)                                    7.21                 
 Core              User (user)                                                7.21                 
 Custom            custom_tweaks (custom_tweaks)                              7.x-0.1              
 Date/Time         Date (date)                                                7.x-2.6              
 Date/Time         Date API (date_api)                                        7.x-2.6              
 Date/Time         Date Popup (date_popup)                                    7.x-2.6              
 Date/Time         Date Views (date_views)                                    7.x-2.6              
 Development       Devel (devel)                                              7.x-1.3              
 Development       Form API Validation (fapi_validation)                      7.x-2.0              
 Domain Access     Domain Access (domain)                                     7.x-3.8              
 Domain Access     Domain Blocks (domain_blocks)                              7.x-2.0              
 Domain Access     Domain Bonus: Login restict (domain_bonus_login_restrict)  7.x-1.0-alpha1       
 Domain Access     Domain Configuration (domain_conf)                         7.x-3.8              
 Domain Access     Domain Context (domaincontext)                             7.x-1.0-alpha1       
 Domain Access     Domain Theme (domain_theme)                                7.x-3.8              
 Domain Access     Domain Views (domain_views)                                7.x-1.5              
 Fields            Fences (fences)                                            7.x-1.0              
 Fields            Fieldgroup (field_group)                                   7.x-1.1              
 Fields            Maxlength (maxlength)                                      7.x-3.0-beta1        
 Jammer            Content Form Jammer (jammer)                               7.x-1.3              
 Location          GMap (gmap)                                                7.x-2.5-alpha4+1-dev 
 Location          GMap Location (gmap_location)                              7.x-2.5-alpha4+1-dev 
 Location          GMap Macro Builder (gmap_macro_builder)                    7.x-2.5-alpha4+1-dev 
 Location          Location (location)                                        7.x-3.0-alpha6       
 Location          User Locations (location_user)                             7.x-3.0-alpha6       
 Mail              Maillog / Mail Developer (maillog)                         7.x-1.x-dev          
 Multilingual      Localization update (l10n_update)                          7.x-1.0-beta3        
 Other             Absolute Messages (absolute_messages)                      7.x-1.3              
 Other             Empty Page (empty_page)                                    7.x-1.0              
 Other             Menu Block (menu_block)                                    7.x-2.3              
 Other             Menu breadcrumb (menu_breadcrumb)                          7.x-1.3              
 Other             Nice Menus (nice_menus)                                    7.x-2.1              
 Other             Node clone (clone)                                         7.x-1.0-rc1          
 Other             Postal Code Validation (postal_code_validation)            7.x-1.2              
 Other             Real name (realname)                                       7.x-1.1              
 Other             Term Reference Tree (term_reference_tree)                  7.x-1.9              
 Other             Token (token)                                              7.x-1.5              
 Registration      Registration role (registration_role)                      7.x-1.0              
 SEO               Page Title (page_title)                                    7.x-2.7              
 Theme Tools       Omega Tools (omega_tools)                                  7.x-3.0-rc4          
 User interface    jQuery plugins (jquery_plugin)                             7.x-1.0              
 Views             Better Exposed Filters (better_exposed_filters)            7.x-3.0-beta3        
 Views             Views (views)                                              7.x-3.6              
 Views             Views Fluid Grid (views_fluid_grid)                        7.x-3.0              
 Views             Views UI (views_ui)                                        7.x-3.6              
 Webform           Webform (webform)                                          7.x-3.18   

Still very annoying though but willing to debug this any further.

Thanks for a great theme anyway !

Are you using Omega 3.x or 4.x? I can see that you have Omega Tools installed, hence my question. Omega Tools is _not_ compatible with Omega 4.x because it does the same things that 4.x solves in the theme layer nowadays (like drush integration, etc.). Please do not use Omega Tools with Omega 4.x. I might write a 4.x version of Omega Tools soon with a UI wizard for creating subthemes again but right now it's incompatible.

Anyways, that's not causing the problem... I was just wondering if you are using 4.x!

Using Omega 3.x

I have also seen this happen on multiple occasions, with Omega 3.x. Currently I can reproduce it on a Domain Access site by clearing all caches on a non-default domain which uses a different locale than the other domains.

 Administration               Administration Development tools              Module  Enabled        7.x-3.0-rc4   
                              (admin_devel)                                                                      
 Administration               Administration menu (admin_menu)              Module  Enabled        7.x-3.0-rc4   
 Administration               Administration menu Toolbar style             Module  Enabled        7.x-3.0-rc4   
                              (admin_menu_toolbar)                                                               
 Chaos tool suite             Chaos tools (ctools)                          Module  Enabled        7.x-1.3       
 Core                         Block (block)                                 Module  Enabled        7.22          
 Core                         Blog (blog)                                   Module  Enabled        7.22          
 Core                         Comment (comment)                             Module  Enabled        7.22          
 Core                         Contact (contact)                             Module  Enabled        7.22          
 Core                         Content translation (translation)             Module  Enabled        7.22          
 Core                         Database logging (dblog)                      Module  Enabled        7.22          
 Core                         Field (field)                                 Module  Enabled        7.22          
 Core                         Field SQL storage (field_sql_storage)         Module  Enabled        7.22          
 Core                         Field UI (field_ui)                           Module  Enabled        7.22          
 Core                         File (file)                                   Module  Enabled        7.22          
 Core                         Filter (filter)                               Module  Enabled        7.22          
 Core                         Help (help)                                   Module  Enabled        7.22          
 Core                         Image (image)                                 Module  Enabled        7.22          
 Core                         List (list)                                   Module  Enabled        7.22          
 Core                         Locale (locale)                               Module  Enabled        7.22          
 Core                         Menu (menu)                                   Module  Enabled        7.22          
 Core                         Node (node)                                   Module  Enabled        7.22          
 Core                         Number (number)                               Module  Enabled        7.22          
 Core                         Options (options)                             Module  Enabled        7.22          
 Core                         Path (path)                                   Module  Enabled        7.22          
 Core                         Search (search)                               Module  Enabled        7.22          
 Core                         Statistics (statistics)                       Module  Enabled        7.22          
 Core                         Syslog (syslog)                               Module  Enabled        7.22          
 Core                         System (system)                               Module  Enabled        7.22          
 Core                         Taxonomy (taxonomy)                           Module  Enabled        7.22          
 Core                         Text (text)                                   Module  Enabled        7.22          
 Core                         Update manager (update)                       Module  Enabled        7.22          
 Core                         User (user)                                   Module  Enabled        7.22          
 Date/Time                    Date (date)                                   Module  Enabled        7.x-2.6       
 Date/Time                    Date API (date_api)                           Module  Enabled        7.x-2.6       
 Date/Time                    Date Migration (date_migrate)                 Module  Enabled        7.x-2.6       
 Date/Time                    Date Popup (date_popup)                       Module  Enabled        7.x-2.6       
 Date/Time                    Date Repeat API (date_repeat)                 Module  Enabled        7.x-2.6       
 Date/Time                    Date Repeat Field (date_repeat_field)         Module  Enabled        7.x-2.6       
 Date/Time                    Date Views (date_views)                       Module  Enabled        7.x-2.6       
 Development                  Devel (devel)                                 Module  Enabled        7.x-1.3       
 Development                  Migrate (migrate)                             Module  Enabled        7.x-2.5       
 Development                  Migrate Extras (migrate_extras)               Module  Enabled        7.x-2.5       
 Development                  Migrate Sziget360 (migrate_sziget)            Module  Enabled                      
 Development                  Migrate UI (migrate_ui)                       Module  Enabled        7.x-2.5       
 Domain                       Domain Locale (domain_locale)                 Module  Enabled        7.x-1.0-alpha 
                                                                                                   4             
 Domain Access                Domain Access (domain)                        Module  Enabled        7.x-3.9       
 Domain Access                Domain Alias (domain_alias)                   Module  Enabled        7.x-3.9       
 Domain Access                Domain Blocks (domain_blocks)                 Module  Enabled        7.x-3.0-alpha 
                                                                                                   1             
 Domain Access                Domain Configuration (domain_conf)            Module  Enabled        7.x-3.9       
 Domain Access                Domain Content (domain_content)               Module  Enabled        7.x-3.9       
 Domain Access                Domain Fields (domain_fields)                 Module  Enabled        7.x-1.0-beta1 
 Domain Access                Domain Settings (domain_settings)             Module  Enabled        7.x-3.9       
 Domain Access                Domain Taxonomy (domain_taxonomy)             Module  Enabled        7.x-3.x-dev   
 Domain Access                Domain Theme (domain_theme)                   Module  Enabled        7.x-3.9       
 Domain Access                Domain Views (domain_views)                   Module  Enabled        7.x-1.5       
 Fields                       Computed Field (computed_field)               Module  Enabled        7.x-1.0-beta1 
 Fields                       Fieldgroup (field_group)                      Module  Enabled        7.x-1.1       
 Fields                       File (Field) Paths (filefield_paths)          Module  Enabled        7.x-1.0-beta3 
 Fields                       Link (link)                                   Module  Enabled        7.x-1.1       
 Filter                       simplehtmldom API (simplehtmldom)             Module  Enabled        7.x-1.12      
 Media                        Derivatives API preset UI                     Module  Enabled        7.x-1.0-beta1 
                              (media_derivatives_ui)                                               +14-dev       
 Media                        File entity (file_entity)                     Module  Enabled        7.x-2.0-unsta 
                                                                                                   ble7          
 Media                        Filters Image Effect (filtersie) (filtersie)  Module  Enabled        7.x-1.0       
 Media                        Image styles admin (image_styles_admin)       Module  Enabled        7.x-1.1       
 Media                        Imagecache Actions (imagecache_actions)       Module  Enabled        7.x-1.1       
 Media                        Imagecache Canvas Actions                     Module  Enabled        7.x-1.1       
                              (imagecache_canvasactions)                                                         
 Media                        Imagecache Custom Actions                     Module  Enabled        7.x-1.1       
                              (imagecache_customactions)                                                         
 Media                        krpanotools engine (media_krpanotools)        Module  Enabled                      
 Media                        Media (media)                                 Module  Enabled        7.x-2.0-unsta 
                                                                                                   ble7          
 Media                        Media derivatives (media_derivatives)         Module  Enabled        7.x-1.0-beta1 
                                                                                                   +14-dev       
 Meta tags                    Domains meta tag (domains_metatag)            Module  Enabled        7.x-1.1       
 Meta tags                    Meta tags (metatag)                           Module  Enabled        7.x-1.0-beta5 
 Meta tags                    Meta tags: Dublin Core (metatag_dc)           Module  Enabled        7.x-1.0-beta5 
 Meta tags                    Meta tags: Open Graph (metatag_opengraph)     Module  Enabled        7.x-1.0-beta5 
 Multilingual -               Block languages (i18n_block)                  Module  Enabled        7.x-1.8       
 Internationalization                                                                                            
 Multilingual -               Contact translation (i18n_contact)            Module  Enabled        7.x-1.8       
 Internationalization                                                                                            
 Multilingual -               Field translation (i18n_field)                Module  Enabled        7.x-1.8       
 Internationalization                                                                                            
 Multilingual -               Internationalization (i18n)                   Module  Enabled        7.x-1.8       
 Internationalization                                                                                            
 Multilingual -               String translation (i18n_string)              Module  Enabled        7.x-1.8       
 Internationalization                                                                                            
 Other                        Background Process (background_process)       Module  Enabled        7.x-1.14      
 Other                        Background Process Apache server status       Module  Enabled        7.x-1.14      
                              (background_process_ass)                                                           
 Other                        Backup and Migrate (backup_migrate)           Module  Enabled        7.x-2.4       
 Other                        Entity API (entity)                           Module  Enabled        7.x-1.0       
 Other                        Entity tokens (entity_token)                  Module  Enabled        7.x-1.0       
 Other                        Mollom (mollom)                               Module  Enabled        7.x-2.4       
 Other                        Panoramas (panorama)                          Module  Enabled        7.x-0.1       
 Other                        Pathauto (pathauto)                           Module  Enabled        7.x-1.2       
 Other                        Progress (progress)                           Module  Enabled        7.x-1.4       
 Other                        Social Share (social_share)                   Module  Enabled        7.x-1.13      
 Other                        Testivals (testivals)                         Module  Enabled        7.x-1.0       
 Other                        Token (token)                                 Module  Enabled        7.x-1.5       
 Other                        Transliteration (transliteration)             Module  Enabled        7.x-3.1       
 Path management              Global Redirect (globalredirect)              Module  Enabled        7.x-1.5       
 Performance and scalability  Boost (boost)                                 Module  Enabled        7.x-1.0-beta2 
 Statistics                   Piwik Web analytics (piwik)                   Module  Enabled        7.x-2.4       
 Taxonomy                     Taxonomy Manager (taxonomy_manager)           Module  Enabled        7.x-1.0-rc2   
 User interface               Add another (addanother)                      Module  Enabled        7.x-2.1       
 User interface               Autocomplete Deluxe (autocomplete_deluxe)     Module  Enabled        7.x-2.0-beta2 
 Variable                     Variable (variable)                           Module  Enabled        7.x-2.2       
 Variable                     Variable admin (variable_admin)               Module  Enabled        7.x-2.2       
 Views                        Views (views)                                 Module  Enabled        7.x-3.6       
 Views                        Views UI (views_ui)                           Module  Enabled        7.x-3.6       
 Other                        Festivals (festivals)                         Theme   Enabled        1.x           

I see that both @undersound3 and myself are using Domain Access, which allows you to set certain options/variables per-domain. Theme settings are among these per-domain options.

On my site, I seem to have fixed the issue by setting the options on /admin/structure/domain/view/[domainid]/theme/[themename]/theme-settings for each separate domain, instead of setting them once on /admin/appearance/settings/[themename]

here, I am using omega4, and no domain access :)

Happen on my site with Omega theme, features and deltas modules. After clear cache, the site settings revert to whatever I store in features. It's like the settings never get stored in db.

I still can't reproduce this and it's been a long time since the last (actual) comment on this issue. Please re-open if you are still encountering this problem. It looks like it's been silently fixed though.

I met same issues with a subtheme of omega 4.0.
Clearly, I lost the settings of my subtheme and of my custom layout when i save some settings in Mail system module (even if I don't change anything). I can saw the content, but all the regions seem to be unavailable. If i clear the cache right after, everything is OK.

I have in the logs this error :

Notice : Undefined variable: row_attributes dans include() (ligne 12 dans .../sites/all/themes/omega/omega/templates/views/views-view-unformatted.tpl.php).

After clearing the cache, the error don't appear.

Sometime, the bug appear after clearing the cache, or after set some settings on permissions (so after a clear cache too)

To reproduce the bug, you can install Mail system and then save some settings in this Module.
You should then see that the subtheme lost the regions.

Below an overview of the markup with the bug

<div class="l-page">
<header class="l-header" role="banner">
<div class="l-branding"> </div>
<div>
<div>
<h2>
<div class="contextual-links-wrapper contextual-links-processed">
<div>
</div>
<div>
<div class="contextual-links-wrapper contextual-links-processed">
<div>
</div>
<div>
<div class="contextual-links-wrapper contextual-links-processed">
<div>
</div>
<div>
<div class="contextual-links-wrapper contextual-links-processed">
<div>
</div>
</div>
</header>
<div class="l-main"> 

And after a clear cache, the normal markup

<div class="contextual-links-region l-page has-no-sidebars">
<div class="l-wrapper-header">
<header class="l-header" role="banner">
<div class="l-branding"> </div>
<div class="l-region l-region--navigation">
<nav id="block-system-user-menu" class="block block--system contextual-links-region block--menu block--system-user-menu" role="navigation">
<div class="responsive-menus responsive-menus-0-0" data-mediasize="768">
<div id="block-delta-blocks-logo" class="block block--delta-blocks contextual-links-region block--delta-blocks-logo">
<div id="block-delta-blocks-site-name" class="block block--delta-blocks contextual-links-region block--delta-blocks-site-name">
</div>
</header>
</div>
<div class="l-main"> 

Any idea ?

Origin of this issue seems to be the MailSystem module
See https://drupal.org/node/2051135
If i select in the settings the "current" theme, theme everything is OK
The bug occurs when i select a theme specificaly.

Patch provided in https://drupal.org/node/2051135 solved my issue.

Same issue here as well. If anything clears the cache, I lose all my theme settings. So, I don't think it's the mail system module. The mail system module is probably just clearing the cache for some reason.

That being said, our Dev server runs on Nginx, this behavior is not apparent in there. This behavior is only apparent in Apache running PHP 5+, which is mine, and another developer's working on the site, local dev environment.

EDIT:

Just noticed this only happens when using Drush. If I clear Caches from admin/config/development/performance it's totally fine. So, I don't know what the heck is going on. Maybe someone who's much smarter than me can figure this out.

Had the same issue with our sub-theme settings being reset each time the cache was cleared (we are using domain access). Following the advice given on this page fixed the issue for us http://www.drupalden.co.uk/domain-access-cant-configure-each-sites-theme.... Copied here:

"Firstly ensure that you have the Domain Theme module enabled - not just Domain Access!

​"Don't try change each sites theme settings via Appearance > Settings. That works fine when setting your Global Theme settings, but it doesn't work the same as setting each sites System > Site information, ie. by logging into each site and going to that page and saving.

"To change each sites theme settings go to the Domain config page (/admin/structure/domain), and edit the site you want to change via the edit domain link. Within that area you will notice that there is a Themes tab. In there you will be able to configure each sites theme settings."

I notice the same fix worked for ahoeben as well.

This issue is caused by Mail System and it is fixed in the dev version.