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I had this exact same problem. A support ninja suggested I turn off my idisk sync function. I did, and since that point I have not had the problem reoccur. Something about idisk syncing with my local disk fouled up the omnifocus.ofocus file in MobileMe.

After turning off the idisk sync option, I backed up the Omnifocus database, moved the existing folder in MobileMe to a different location and initiated another sync in OmniFocus. I've been problem-free since.

I hope the good folks at OmniFocus can figure this one out so I can get back my sync functionality on idisk.

Robert