It could be the encoder or something on the motherboard, or hopefully just firmware.
I am not certain, but assume that the encoder counts from the home position.
And it appears to find the home position, as it will cut narrow material. So it is finding the first two rollers, if my understanding is correct, but it will not locate the 3rd in it's normal detent position.
Which would indicate lost counts or the movement is not what it should be.
That is why I am hope a firmware reinstall may be able to reset every thing and recover tracking.
If not, perhaps the belt is stretched just enough so that it is off just enough to miss the last hold down roller.
Minus that, it could be a component on the mainboard that is loosing count.
Really hard to say from here.