Hi,
I think this test is the correct one:
Also, does the Y-axis work using the MDI or the pop up onscreen MPG pendant (press tab key on keyboard)?
If the Y axis does not work under this circumstance when the X,Z and A do then it means most probably a fault on the board, most commonly the stepper driver IC.
I would guess if you had a close look it will be a Toshibe IC 68.... or similar, good ICs if used within their limits and cheap, but tender and prone to failure if you
stray outside those limits.
Can you post a close-up pic of the board and/or driver ICs?
Craig