Have you moved your sync data location into the Backup directory on your iDisk, as is suggested to be the solution for this issue? There isn't any evidence that OmniFocus is hosing your data; it is the MobileMe sync code that is suspect, because when OmniFocus is configured to sync in a location on the iDisk that isn't synced by the MobileMe sync feature, the problem does not recur. You can read about how to do it
here. (Look for the "Tip on using Mobile Me")