We have a dev site working fine with Omega. We transferred the site to a new server, and now the custom regions that were added to the info file are not in the Omega UI. The entries are still there in the info file, but completely gone in the UI. They are not even in the disabled area. File system is fine. Ran cron. Flushed cache.

Deleted and recopied theme files a few times, and the custom regions in the UI show until I flush cache, and then they are gone again.

Comments

Export the theme settings on the first server to code.
Appearance > Settings > Your theme > Export theme settings (on the bottom).

The info files does not change when settings are changed in the GUi.. you need to update it yourself.

That is with Omega Tools, correct?
I know that the contents of the info file are not changed when you change settings in the UI. But when you copy a full site to a different server, how come custom regions are not kept? Pushing files from Server A to Server B, then pushing Server A's db to Server B should not have any effect on Omega settings. It doesn't make sense why you would need Omega Tools just to move a site to a different server.

I export settings on the dev to the ".info" and then tell Drupal to reset the theme - and test again.
Then I commit the theme to GIT on dev and pull it on on live.
But I see your point, if you copy both code and DB from A to B, B must be the same.

Project:Omega» Omega Tools
Version:7.x-3.0» 7.x-3.0-rc4

omega saves settings to the DB so you need to transfer the db too.
if you use omega tools as it seems i move this to omega tools issues.