[whpalmer4]

MobileMe is attempting to sync your OmniFocus database file. You don't want that, as it doesn't understand how to do it properly. You should store your sync database in the Backup directory on the iDisk instead of Documents if you are going to have MobileMe disk sync running. The contents of the Backup directory are ignored by the MobileMe sync.

Your other issue may or may not be related, but you definitely don't want MobileMe doing any syncing of your OmniFocus database. Is it possible that you didn't have MobileMe sync enabled before your upgrade? Turning it off would be another approach, if you don't need it.

The "do you want to replace your database and start syncing" message is only supposed to happen if OmniFocus detects that the sync database (on MobileMe in your case) is newer than the local one, and it might have gotten confused if MobileMe changed your sync database. I would use File->Replace Server Database... to repopulate the server copy from your local copy (I'm assuming here that your local copy has all your changes), and turn off MobileMe disk sync to see if the various warnings go away. If they do, and you want MobileMe disk sync back, then you should move your sync database into the Backup folder -- contact the support ninjas by email or phone and they can walk you through it, if you have questions.