I think you're looking at the wrong thing. Your photos focus on the three black ball through switches. The opto connectors are those white connectors. One side of the optos has a 3 pin connector, and the other side is 2 connectors.
Your comment said: "They were properly seated and soldered".
You can't just visually tell if something is seated properly. You need to pull the connector off, and then just push it back into place. That's what "re-seating" is. Those white IDC connectors are flakey...even on new games. They are for the optos, one which tells if there is a ball ready to be ejected, and another, higher one which tells if a ball is balanced halfway up (ie "jammed").
When a ball is not jammed, the opto shines all the way through. If a ball is jammed, it blocks the opto, and the game knows to try and kick it out into the shooter lane. If the connector loses connection, then the opto does not shine through, and it thinks a ball is jammed, so it tries to kick it out.
So, if the connector is not secure, it will kick out a ball at the start of a ball, then think one is jammed, and then kick out another...and you end up with two balls in the trough.
Re-seat the white connectors by taking them off and putting them back on. This takes 5 seconds to do by hand. In my experience, this will always be a problem until you get rid of the white IDC connectors by soldering the wires directly, or by switching to molex connectors. But for now, you can just reach under and re-seat them to fix the problem of 2 balls in the trough.