This happens very frequently on many sterns. Especially if they get played a bit.
The most likely culprit is one of those trough opto boards. The game's confused as to how many balls are actually in there. The basics first... Go into diagnostics and see if any of the optos or roll overs fail to recognize any of the four balls, or if any stay closed when you empty it. Then try unplugging the opto boards, and reconnecting them. Sometime the connector get heavy vibration, and doesn't make proper contact with the male header pins.
-jon