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Well, I think I can help explain what's going on, but to figure out why, you'll probably want to contact our support ninjas; to figure out what's going on here, we sometimes need to ask for screenshots of system preferences or other stuff you probably don't want to post in a public forum.

It sounds like the special files that OmniFocus uses to tell what devices are syncing with a server database are getting out of whack somehow, which is resulting in your sync information compacting when it really shouldn't do so. Once the database compacts, we lose the ability to insert changes into the sync database - you can only copy one database over the other.

If the 'coalesce database' script that was posted to the forums a couple of months back is getting run frequently, I guess that would be one possibility that could produce these symptoms. If that's not it, though, contacting the support ninjas (please include the info whpalmer4 requested) from the help menu of OmniFocus for Mac would be the way to go.