Swap the motor and use a different known working motor on the y axis. If the problem persists then this rules out the motor.
If not the motor -> Go into EMC2 setup and see which pin controls direction on this motor. Probe that pin on the card with your multimeter. It should read +5v when you tell the motor to spin one way and 0v when you tell the motor to spin the other way.
If motor changes direction without changing signal -> check card for loose connections, its not a computer or motor problem.
If signal changes when its not supposed to -> try a new parallel cord, sometimes they have a bad connection. If not the parallel cord its the computer.