as above
the 1st thing I would do is swap the X and Y driver wires. Then you will know if it is the motor, or something before
If it is something before, and you have a separate BOB, then swap the feed from the BOB to the driver. Then you will know if it is the Driver, or before.
If it is still before, try using a spare axis on the BOB (if you have one) or set the BOB / Mach3 to use different pins on the par cable. Then you know if it';s the BOB or before
if before, then its down to the par cable, the par card/port , or software .
you get the idea ? ... just trace it back, step by step.
HTH
Rich
My 1st Build (ongoing) http://www.cnczone.com/forums/diy-cnc_router_table_machines/134670-one_big_one_smaller_my.html