I would check this circuit, esp. the score motor switch, as well as the stepper unit.

Here is good reading on steppers from Clay's guide: http://www.pinrepair.com/em/index2.htm#steps
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Does the problem happen with all the 300 / 3 adv rollovers? The two rollovers at the top are "when lit" rollers and the bottom right inner rollover will always score 300 / 3 adv. If the problem only happens with the top rollovers, check the ALT relay. If the problem happens with all the rollovers, check the score motor switches that are associated with the 300 / 3 adv relay - score motor switches 6B, 1B, 10B...

11B score motor produces the pulses for both the bonus step up and the 100 point score relay. It produces 5 pulses per score motor cycle. The way Bally does less than 5 is by when exactly the relay drops out. Try holding the relay in, and see if you get 5 and 5 for each half turn of the score motor. If you get less than 5, especially random amounts each time, suspect Score motor switch 11B. If you get 5, 11B is okay and it is when the relay is being dropped out that is the cause of the problem (being dropped out too soon). Super hard to read the IPDB schematic but it looks like this is handled by Score Motor switch 6B.

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