Sounds like you've checked everything fairly well.
- Maybe try connecting a known good remote.
- With no remote connected, manually activate the anti-derail feature in both directions to see if that will move the points.
- Next check continuity individually between the Common and NO and NC terminals on the micro-switches when the micro-switch levers are in both positions.
- If the micro-switches are good, I'd swap in a new motor driver board; cs-691TRC4A01-p
Here's the link to it on Lionel's Parts site:
https://www.lionelsupport.com/...FASTRACK-SWITCH-TMCC
I've had the same exact symptoms. Once it was a wire separated from the micro switch.
Another time, the board was partially bad and was only faulty in the ways you describe. I think it may have been caused by voltage spikes from a derailment.