The only things that come to mind is the wiring to the motor. the phase relationship is important, swapping black for green, etc might make the difference. Be sure all your voltages are right. The stepper driver needs a solid 5V supply to accurately manage the current.
Have you tried taking out all the driver chips except 1, say for the Y axis? If that does or doesn't work, move on to the next Axis, a different driver board, pull out the Y driver so you're only going one axis at a time.