You may have a timing issue here. Try and watch the Reset relay and the Score Reset switch on the Score Motor as you start a game. Note that there is a Reset Relay switch in the path to the Score Reset Relay. That switch, and thus the Reset Relay, has to be made before the Score Motor makes the Score Reset switch. If the cams are worn, or the cam followers and/or switches are adjusted too close or too wide, it may be out of time.
I spent several days a couple weeks back tracking a scoring issue on my Gottlieb 2001. It was scoring 400 points instead of 300 for lit features. Turned out to be a switch on the score motor that was supposed to open the 100 point circuit after a switch on another cam pulsed 3 out of the 5 lobes on that cam. The switch was misadjusted and it opened one lobe too late, allowing another 100 points to ring up.
Timing issues are insidious