I just had a very similar problem on my Earthshaker. The game would see that there were 3 balls in the trough at the start of the game, but whenever a ball was lost in the outhole, the game would kick it over into the trough, but not recognize that the ball was in there. In switch tests, the switch would work intermittently. Turns out, a cold solder joint on the switch was to blame. It looked like it was soldered correctly, but it was not. Reheating and doing switch tests confirmed the fix. Give your switches a good look over, and make sure everything is making good contact.