Start by checking the shooter lane switch for loose wire or diode disconnected or touching where it shouldn't be (if it has a diode). If that doesn't check out go into switch mode and see if it sees the switch activate or is stuck on in switch mode. If it does activate in switch mode you'll need to dig deeper. If it doesn't then you can actually use a probe put in buzz mode to check for continuity, put it across the switch and activate it to see if your meter buzzes. If it buzzes switch is good, dig deeper. If it doesn't buzz you may need a new switch.
But my general feeling here is the switch isn't getting a signal to the board letting it know the ball has kicked out so it kicks out the second one.