I bought a Pistol Poker late last summer. I had the multi-ball issue as well. I pulled my hair out for a while, thinking bad switch, software error, etc. After a multi-ball game there would be 1 and sometimes 2 balls left in the shooter lane when game ended. One day I had the apron off and I was observing the action of the outhole kicker and noticed that kicker was very harsh when kicking the ball over to the ball release mechanism. I also noticed there was some peening on the underside of the apron which suggested that the balls were hopping and hitting it.
So here's the problem, when you have 2 or 3 balls on the playfield and one drains, the trough is empty and the strong kicker would hit so hard that the ball would go too far and end up at the shooter lane release switch. That switch will activate the release coil every time a ball lands on it. If the trough was loaded with 2 or 3 balls, this wouldn't be an issue because the balls cannot jump over the bar with those balls in the way.
When I bough the game the seller was nice enough to give me 3 extra NOS coils. One of which was CLL-004(same coil as the shooter lane release coil). This coil has almost twice the resistance of the CLL-006 which is what the game calls for in the outhole kicker mech. A higher resistant coil has a weaker(softer) action. I swapped the 006 to the 004 and it seems to have eliminated the problem of the balls jumping over the trough bar and so far after about 100 games, the game not lost track of any balls. The CLL-006 coil is way to strong for what it needs to do IMO. It only has to move the ball about 6-8 inches, but it's strong enough to be used on a sling or pop bumper.
I hope many of you can try this and report on your results.