Had this same problem the other day, but LTG's fix worked for me. I'd take off the apron and watch the balls cycle through to make sure everything is running through smoothly. My balls fire a bit too hard through the trough, so I had to make sure the wires from my switches were high enough to prevent balls kicking back off of the others and therefore triggering the switches too many times.
Also, check your diodes on all of your trough switches.
Good luck.