There will be no magic involved and finding situations where the error doesn't occur rarely helps to narrow down what's causing it where it does. Assuming you have some matching drivers in your system swap one over with the Y and see if the fault stays with the axis or follows the driver, ditto the motor. You can test your break out board by swapping X and Y outputs and swapping pin out config in Mach3 and seeing if the fault stays with the axis or moves with the BOB output.
If the fault isn't in the electrics then it's mechanical.

- Nick