Since it happens on single and double bonus and yet it is giving you the correct points, I would think the score motor is struggling or slipping but still successfully completing it's cycle. When you knock a drop target down for 500 pts, is the cadence also unusual? How about when you reset the game - do the score reels reset with the non-uniform cadence?

So if the score motor is running smoothly, then it is most likely the bonus circuit, and as HowardR pointed out, specifically the Bonus Unit Reset Solenoid circuit. If all the circuit switches (Bonus Score Re., A Re., B Re., 2B SCM) check out good (clean contacts, check gap, and verify continuity when closed), then look at the unit itself. Yes, that is the bonus unit on the underside of the playfield. The unit has 2 solenoids on it - the Reset solenoid is the one furthest away from the playfield. You can manually step it up and down (with the power off), and I suspect you will find it is sticking on the way down (Reset solenoid). These units notoriously gunk up after 40+ years and the entire unit requires rebuilding to get their "snap action" back. It might also not quite be assembled correctly or have a weak spring or otherwise be out of adjustment in some way. Another possibility is that both of the solenoids on the bonus unit are energizing simultaneously intermittently (due to a short) which would have the same result as a sticking Reset (no decrement).

Not sure if you know this or not, but you can't measure the resistance of a coil when it is installed in a machine and have any faith that the result is accurate. You have to desolder one leg of the coil.