I had a similar issue with trough switches and was getting the issue with multiple balls launching. Couldn't work out what it was 0 everything looked okay - turned out that a small bug had been squished under one of the trough switches itself - when the ball landed on it, it would register but when it rolled forward the switch would stick to the squished bug for a few seconds before it would flick back up - I doubt there's a squished bug in yours but you might have a sticky or intermittent microswitch in your ball trough.