I went back in and tried to do a full update with verify. The "Dot-Matrix" update text would flash on and off over the top of the Stern logo screen that still said "restarting game". It wasn't easy to read and make out, but I got the full install going.
That seemed to fix it, and it booted up after that. So the quick update is broken. Of course, I lost Cleland's sounds with the full update.
What's worse is some of the changes to the game. The right orbit shot now no longer drops into the pops during modes. When you shoot the ball in the scoop, it shoots out faster and doesn't have the sound to accompany the flashing light.
This update is shit. I'm going back to 1.04.