On my remote server:
- Changing the settings in admin/settings/appearance/subtheme do not save (i.e. I do not get a "your changes have been saved" confirmation).
- Changing the settings in admin/settings/appearance/omega do not save.
- Changing the settings in admin/settings/appearance/alpha DO save (I get the confirmation message).
On my local machine (MAMP), all settings for all omega-related themes (subtheme, etc) save just fine.
My only conclusion would be that it is the remote server setup that is to blame (file permissions, etc), but the fact that the alpha theme takes hold of the changes no problem makes me think twice about that conclusion.
I've checked all the file permissions and nothing seems out of place. The file owners and groups are the same for subtheme, omega, and alpha.
I've seen some other issues (#1179006: UI LAYOUT SETTINGS > Primary layout - cannot disable layouts, #1218126: If I deactivate the breadcrumbs admin/appearance/settings/MYSUBTHEME after save they're on again) that address similar problems, but there isn't much detail on the fixes.
Not expecting a server diagnosis here, but any ideas would help - because at this point I haven't got much hair left to pull out ; )