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Sorry about the unclear error message! We'll try to come up with something more understandable.

The "root" transaction is the first transaction written to your OmniFocus database, and this error indicates that something has deleted that first transaction. I don't think there's any way for OmniFocus to do this itself (it writes everything to a temporary location and then moves it into place so that another copy won't see a partially written database), so my guess is that something else is deleting those transaction files.

Perhaps something else is trying to synchronize an old copy of the entire folder that the database lives in, and ends up removing transactions? I guess it's possible that iDisk offline syncing might do this, although I don't know why it would think that an older copy of that folder without transactions should replace a newer copy with them.

If you're seeing this error, could you confirm whether you have iDisk Sync turned on in your MobileMe (or .Mac) preferences, and whether turning that off fixes the issue? Thanks!