It's likely that one of the balls is stuck somewhere. I had a similar issue on mine (an LE) and found a ball stuck in the upper play field area in between the upper and lower play field caught on some wires...it was a bitch to find it and get it out.
Double check to make sure all 6 balls are in the trough...its strange as the game did not state that there was a ball missing.
Good luck!
Ed