I'm having trouble understanding the problem and the solution. Can anyone elaborate? Is the problem that the Lightbox Advance Zero Position switches change state while the ball rolls over the Trough switch so both units step down, almost simultaneously? Or is the problem that the Lightbox Advance Unit steps down before the ball is kicked to the shooter lane, and that the Ball Count steps down once the Trough switch closes?

/Mark

If the Lightbox Advance unit steped down before the Trough switch closed that implies that a Score Motor switch caused it to step down. Looking at the schematic, I don't think the Lightbox Advance unit should ever step down because of a Score Motor switch, unless you've tilted and the H/Tilt Hold relay switch allows pulses from Motor 2C to get through. (Note that the H relay switch is shown as normally closed because the schematic is usually drawn with the game unplugged. When the game is on the H/Tilt Hold relay is usually active and that switch would be open.)
Team One Subtract Ball Count 3 (resized).jpg
If the problem only happens on the last ball, that implies that it's using the 5th position Ball Count Unit switch in the red box and the Motor 4B switch next to it. But if the Zero Position Lightbox Advance Make/Break switch (other red box) is working there should be no way for that pulse to get through to the Subtract Lightbox Advance Unit solenoid.

What may have been happening is that the Make/Break switch was actually closed on both sides which would have created a path from the Motor 4B switch to the Subtract Lightbox Advance Unit solenoid. Adjusting that switch may have made it "break before make" as it should so there is never a path between the two outer leaves.

The solution to the problem is the same (adjust the switch) but I think the reason is different than a timing issue. You could test the theory by jumpering the two outside leaves of that Make/Break switch together to see if the problem reappears.