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Dave, I'm sorry for the trouble this is causing! I just heard from one of the engineers - it turns out if the iPad went to sleep while OmniFocus was in the background, updates like this could get delayed. They don't stop, but they will fire late.

We don't want to delay the version that's currently in Apple's review pipeline by pulling the release to add this, but we will get it fixed in an update. Sorry for the trouble.