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I'm doing daily 3 way syncs with the all three client types and occasionally have this issue. But since I ALWAYS sync before I do any work in omnifocus and then after, I always know whether to keep the local or remote database so it's not a big issue.

(I sync using MobileMe and have iDisc syncing turned on)

Does anyone know:
a) How/Why omnifocus believes the databases are incompatible?
b) If there are any known scenarios that trigger it?

I have noticed that my iPhone clock can drift a few minutes a month and wondered if out of order timestamps might be a factor.