The circuit to fire the Game Over trip relay at the end of the game goes through three switches and the Ball Count stepper in red:
Super Star Game Over trip relay (resized).jpg
If the Ball Release solenoid works after the ball drains the Outhole relay switch is probably good. If the Ball Count works during the game the Ball Index relay switch is probably good. That leaves the Score Motor 1-A switch and the Ball Count Stepper as likely culprits.

"Seems good" probably isn't good enough. You need to prove that a device is working before dismissing it as a possible culprit.

/Mark

I had a similar odd problem with a "Super Star" just last week.
As soon as the toggle switch under the game was turned on, the score reels would reset (the game remaining dark). I noticed that if I manually tripped the "game relay" first, it wouldn't do it.
I did not have a schematic, and was about to ask for help here, but I cleaned all the switches on the game relay, and game over relay again. Now the game relay trips as it should, and the issue is fixed.

interesting update here. with ball 5 drained and game over illuminated, game still spits out a ball to play and you can score and use flippers. if i turn the cabinet switch off underneith and turn it back on, all lights (playfield and head) are off but the flippers and playfield switches/targets are still active, even with all lights off....somehow it seeems anytime the cabinet switch is on, the playfield is live (sometimes with lights, sometimes without).

Most games have a switch or two along the power rail from the transformer that cuts power to most of the game after Game Over. Here are Super Star's switches:
Super Star Game Over power switch (resized).jpg
If the switch in the red box doesn't open power will get to the flippers and other parts of the game after game over.