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Sorry for the trouble here, Rob. I suspect what's going on here is that there's a corrupt transaction file in the server DB. That's why the error messages come back after a sync.

When an updated version of OmniFocus is launched, it invalidates the cache and builds a new one from your transaction files. 1.8.2 uncovered the bad transaction during the rebuild, in other words, but it didn't do anything new to your data. This happened to be the first rebuild since the transaction file went bad.

That bad transaction file is preventing OmniFocus from completing the rebuild, but that's all the error message means - that the rebuild can't finish. Repairing the database needs to be done manually, but I'm getting you some help.