I had the same problem NM; mine was a loose IDC connector to the trough optos. (Damn you shaker motor!!! ) Re-seat the two connectors (one on each side) and see if that fixes it. (Simple, right?) (Also, I checked and re-seated the wires going to the connectors too.) If that doesn't do the trick, LTG's answer could be the next step.
I always seem to forget to re-seat those trough connectors when setting the game up initially...