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I have yet to see any suggestion from Omni that they consider it a good idea to have MobileMe's iDisk sync feature turned on if you are using MobileMe as your WebDAV server. There have been problems reported in the past, and while it should work in theory, in practice, life hasn't always been so kind. OmniFocus communicates directly with the MobileMe WebDAV server, so as soon as a change is synced from OmniFocus, what MobileMe has and what your computer has are two different things, and a bug may cause overwriting new data with old.

If you don't really need to have a local copy of your iDisk stored on your computer (and if it is a desktop, you probably don't), you might give some consideration to turning that feature off.