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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.