Mks Gen 1.4 motor issue

I have finally finished squaring up and building yhe primo with my BOI. Flashed dual endstop FW to our MKS Gen 1.4.X an Z are working beautifully, but in Y only 1 motor works. We tried swapping X and Y, which works, thereby eliminating hardware issues. Only one of the horizontal axis will run both motors at a time, regardless of which axis we swap on the board, either X or Z. Do we have a FW issue? Used the Ramps dual endstop Marlin FW