You’ve check the encoder couplings right?
If motor end shaft mount, check for loose set screws or set screw type.
If that cylindrical spring type is used, complete removal will show any break in the coiled section. This type of encoder is know for directional errors when breakage occurs.

Is front door pre opening (CSW1 bit4) Reset? If so, set it to eliminate pre opening as your trouble seems like it’s yet in the “leveling zone”..

You’re not reporting door/gate lock faults, but they may only appear when outside of MLV parameters. Could it be a lock or locks are being blipped off the clutch once drive motion is dictated and doors are initially closed, but your still under the MLV setting when this event (door lock opened) occurs?

Do you see any excessive upward roll back when down direction is commanded and brake lifts?

What “other faults” have been appearing?