Quoted from silver_spinner:as an owner of many sterns and work on many sterns almost daily (old and new):
1) replace the connectors that go to both trough boards (thanks parker).
2) solder everything, not just the pins on the trough boards. doesnt matter if game is new out of box, the trough boards are NOT new. I bought a NIB SEGA harley davison and the optos' solder joints to the motorcycle already were cracked and didnt work properly on game number 1 played.
3) check your weldement at top of trough kick out. if its cracked, broke/raised up, a ball can shootout and fall back in from the shooter lane, then it kicks out 2 balls because 2 balls are now in the up kicker part of trough.
*if you do all of the above and the problem Does not go go away, one or both of your trough pcb has a real problem. replace those and you are done.
In addition to #3, it also could be that the ball is trying to kickout but the angled part at the trough exit is knocking the ball back down causing two balls to be in the jam opto area and thus both balls would be ejected to the shooter lane. This is a common problem and the solution is to bend the angled part slightly either toward the plunger or away from the plunger. It takes some trial and error to get it right.