My sttng had the same issue during ferengi multiball mode. I would have two balls in play, but if one drained, then it would end that ball, even thought I had one in play.
My issue was the LED board in the ball trough, but you have new boards. I would eject all balls, then go into switch test mode and feed the balls one by one into the trough to make sure the switches are responsive to the balls.