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Sorry for the trouble! When a repeating action is checked off on more than one device while they're out of sync, it produces the results you're seeing. This happens because each device makes a new "next" copy of the action, then inherits the one from the other device when they're brought back into sync. Any chance that's what is happening here?

Theoretically, we could prevent this by inspecting new actions during the sync process, but that would have the consequence of making all your syncs slower and take longer to complete. Thus far, we haven't wanted to take that performance hit.

If you'd like to minimize the chances of this happening, just go ahead and sync the device you're switching away from, then sync the device you're about to start using OmniFocus on. This ensures that your devices are always working with the most up-to-date info in your database and minimizes the chance of a situation like I described above.