Nice! I don't like having no good explanation for a fix, but in a case like that I have to assume it's a bad connection. If it persists, you'll have to narrow down which connector is the culprit and reflow the header pins etc.
As far as the multiball issue: you want to make sure that all 3 switches in the ball trough under the apron (the cover over the ball trough/outhole area below the flippers) are ok. I know that's not where the balls are getting locked, but the game needs to know where the balls are between the capture/locks on the playfield and in the ball trough under the apron, otherwise it will assume it's still in play (afaik). Test with 3 balls, then remove 1, test again, remove another, test again. Experiment a bit, and see if you can get a ball to hang up in that area. I was reading that those switches can be difficult to get adjusted just right.
My theory is that the wire actuator for one or more of those switches may be preventing a single ball from rolling all the way down onto the switch it's supposed to be sitting on. With the weight of one or 2 more balls behind the "next" ball, there's enough force to push through the mis-adjusted switch actuators, but with just one ball it may not be quite enough on its own (and may hang out between 2 switches instead of resting on the one it's supposed to be on).
I'm thinking in this case, it's working fine as long as there's more than one ball in the Outhole Ejector trough--the weight of the extra ball or 2 is pushing the front ball into position, but once you've locked 2 balls--there's no extra weight to push the ball into the switch, so the game doesn't know the ball is there... So it's hopefully a matter of tweaking the switch actuator(s) just right so they allow the ball to roll all the way down without "help" from the other balls.
Again, that's just my guess at this point, but there appears to be some precedent for issues in that area.
You're getting close!!!
Btw, let me know if there's anything I can do to help verify you.