As for my issue, this seems to be a definite bug. I was able to recreate this several times with the glass off. When the ball kicked out of the lower part of the trough at the exact moment the other ball fell into the exit chamber kickout hole, the exit chamber did not score or advance, and the ball did not kick out. It just sat in the hole with the background music playing. I wonder if it's an issue with the Alltek board, or if it happens on an original MPU as well?
Also, I pulled off the cutoff switch, and there are 4 wires attached. a blue wire and a brown wire, which goes to the line filter, and a black wire and a white wire, which appears to go to the service outlet in the bottom of the cabinet. I was able to jam the button down with an allen wrench to hold the button in, then I placed a screw across the opening on both tabs. I would like to take the switch completely off, however. Maybe I can Crazy Glue the button in?