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Sorry for the trouble, Nathan - you've correctly diagnosed the problem. OmniFocus is trying to sync when the network connection hasn't been re-established yet.

By the time that sync fails and the dialog is dismissed, the connection is usually working. We've got an item filed in the development database on handling this more gracefully, but it hasn't made it to the top of the to-do list yet. I'll attach you to that item, so the rest of the team will know you'd like to see this happen. (The number of customers requesting a change influences our planning; more customers, more likely, all other things being equal.)