Hmm. This is tricky because the only way I can see that happening is that two things would need to be misbehaving. Not impossible, but not common either. The way it should work I believe is:
- the Ball Index relay fires and holds when the first 10 or 100 points are scored
- when the ball drains the Outhole relay fires which immediately starts the Score Motor
- when Score Motor switch 3B activates it should kick the ball to the shooter lane and simultaneously let the Ball Index relay relax
- when Score Motor switch 5B activates the Outhole relay should relax
- the Score Motor should continue turning until the Index B switch opens at the end of one cycle

Part of the puzzle will be to figure out why the Score Motor runs through two cycles. It may be either that the Outhole relay isn't relaxing reliably when the Score Motor 5B switch opens or that the Score Motor doesn't stop quickly enough before starting a 2nd cycle. When it runs through two cycles does it stop briefly between cycles (Score Motor issue) or does it run continuously through two cycles (possibly because the Outhole relay doesn't relax)?

When a ball is skipped and the Score Motor runs through two cycles, when does the Outhole kicker fire? First cycle, second cycle or both cycles?

Even if the Score Motor runs through two cycles the normally open switch on the Ball Index relay should prevent the second cycle from advancing the Ball Count unless that switch isn't opening reliably.

If you're not already you may want to prop up the playfield and simulate the game while watching the Score Motor, Outhole relay and Ball Index relay. Add 10 points, close the Outhole switch, watch the relays to see if the next ball is skipped. Repeat.

Or you could wire a bulb tester (two 12 volt automotive bulbs wired in series) to the Outhole or Ball Index relay coil solder lugs to "see" when they're active.

/Mark