Y axis not moving during break in

Hello. Need help with the break in program. I was able to home the machine with no problem. X and Y axis seem to be working fine when jogging. When opening the break in program and running it, the X axis moves but the Y axis does not. Any advice would be much appreciated.

Well after calling @Langmuir, by the way they are great and easy to get a hold of, I was able to troubleshoot the binding I was getting on the Y axis. I re adjusted the ball screws, made sure everything was squared, re adjusted the limit switches, adjusted the belt tension, oiled the ball screw assembly (I had previously greased them) and loosen the SHCS on the rear rail mounts and snugged them. I think I may have tighten them a little too much. I was able to run the machine at 400ipm no problem. Not sure what fixed it but I am glad that its running smoothly!