X-axis problem on breakin program

After I home the gantry. I then run the break in and the y axis runs completely fine, but the x axis just barely passes the halfway. When it begins to go back to the top left corner, the x axis hits the stop at least 15 inches before the y axis. Also when jogging from the corner, on the Fire control app, it shows the x axis on zero. I move it towards the end and stops a bit before the half way line. Once it stops it shows that the x axis is now 47 and when i go back towards the zero the machine hits the corner and it says the x axis is 10.

Check to see if your coupler is slipping. I made marks on the lead screws and couplers to make sure it’s not slipping.

No, not slipping,
It give a Warning The loaded program extends beyond the machine travel limits

Check all your motor plugs on the electronic enclosure, Make sure they and seeded tight.
the retaining screws can sometime hold the connector somewhat out of the socket.