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I agree with Bill; this sounds an awful lot like the error dialog MobileMe pops up when it thinks there's a conflict with its iDisk Sync. Note that OmniFocus does not use MobileMe's iDisk Sync. OmniFocus uses its own syncing engine and just uses your iDisk as remote storage.

Could you maybe post a screenshot of the dialog, Lightstorm?

Here's a bit of background on the problem with MobileMe's iDisk Sync getting confused about the OmniFocus database.

Hope this helps.