Originally Posted by
maver1ck
There are a number of things that can cause this.
First, the alignment is done based on a signal from the spindle motor encoder (or resolver depending on vintage) so there could easily be an issue with the encoder/resolver, drive/drive controller card, or cable (since the cable flexes in the cable track, they can fail over time).
Depending on the spindle option, it may also have a prox switch mounted at the spindle to confirm orientation. If this switch fails (or the cable to it), the machine will not be able to align.