If it's not displaying a limit switch on the Y axis and the motor has lost power in one direction (take the cover off the Y belt and see if you can turn the pulley in one direction only with the servos on), then I'd put money on an opto isolator.
The other thing to try would be to make sure you are near centre of travel for X & Y, then swap the plugs to the dual axis cards (AC2-P1 & AC2-P2) to check if the board output is there.
If that doesn't work then optos. Behind the card rack in the bottom of the cabinet is a small board with six little chips on (H11G2). it'll be one of the middle two of these.
They are easy to get and cheap.