The first problem was that the elevator would overshoot the 2nd floor. In up direction it would re-level and correct itself in down direction it overshot too much and fault out. I disabled all the 2nd floor hall/car calls so they could use the elevator to get from 1 to 3.
I replaced the encoder, the encoder board, and the neuron piggy back board on the encoder board and kept the old software chip. Now the elevator overshoots all floors and faults out on 1 & 2. I put everything back the way it was, and nothing changes. (I then put all the new boards back, but left the original encoder bc I verified it had +4.9v and had a count on A and B.
The D4 led (slow down indicator) on the encoder board does not blink until it's on the magnets. On the other elevators it blinks before it sees the magnet.

The odd thing is that I have had this same problem on 2 other elevators at the same building. I ended up replacing the encoder board on the car top, along with the neuron piggy back board. (I used the original chip in the new neuron board). I also replaced the encoder for good measure. This fixed the problem in both of the other elevators.

Any chance this could be the car top board?

Any help would be appreciated!!