[whpalmer4]

You didn't answer my question about *how* you are shutting down the computer. Shut Down... command under the apple menu, holding down the power button, yanking the plug out of the wall, what?

Probably you'll want to contact the Omni support folks via Help->Send Feedback in the app to get to the bottom of this. They'll probably want to establish that OmniFocus is getting an opportunity to exit gracefully (or determine why it isn't).