Check motor switch 10B. It keeps the 500/3000/5000 bonus hole relays energized. It's the second switch pair from the bottom, stack 10. Should be normally closed and stay that way until the motor turns to open the switch and release the relays.

Brown-white to yellow wire pair.

Is it clean and wiping well?

Yep... same suggestion. Since 3000pt relay is working fine, it could be that motor 2F isn't opening all the way as it goes round. Looks like the 100pt relay isn't getting the clicks from the motor.