First off, do your chimes work? I ask because I want to know if, when you score 500 points, and it doesn't give you 500 points, do you hear 5 distinct strikes of the chime or does the chime count match how many 100's were added to the players score (less than 5)?
You also didn't indicate if it acts the same on player 2.
Trying to narrow down if it is a problem coming from the score motor (which generates the 5 pulse for the 100 point relay) or if it is a failure of the 100 point relay pulsing the score reel, or if it is the score reel skipping and not accurately tracking the pulses it is given.
You stated that the 500 point and add bonus relay energizes as it should. My question would be whether is holds in for a full cycle of the score motor each time or if it appears to be dropping out prematurely on some of the motor cycles? It must hold in for a full cycle each time in order to allow the 5 pulses to get to the 100 point score relay. It should not drop out until just before the score motor comes to rest. You might be able to "feel" this by leaving your finger on the relay switch ladder while watching the score motor. Not so much as to hold it down, but just enough to feel when it releases and hits your finger.
Two things to check on the score reel itself:
The end or stroke switch. This provides a hold circuit to the 100 point relay. It insures that when something energizes the 100 point relay, it holds in for a full stroke of the plunger on the score reel/drum unit. They often break one of the blades thereby eliminating the hold circuit to the score relay.
The anti-reverse blade - a silver finger that rides on the inside of the plastic score reel. This prevents the reel itself from skipping backwards when the plunger goes in to step it forwards. They often get bent when someone cleans the score reel (wiping strongly with a rag) and then it no longer engages with the ratchet teeth under the score reel spokes.
Bonus collect can be a lot more complicated. Is this a game that counts 1000 points for each phase of the score motor? (Slow collecting) or is it a game that counts down 5 bonus for each cycle of the score motor.
Since there are 3 phases of the score motor on a gottlieb, your theory about it being a mis-adjusted switch hold true if the score motor cams turn just slightly out of round causing some edges of the cams to push more or less than others as it turns.