Did you mean to say that the gShield x axis driver is working and the Y axis driver is working? Because when hooking it up to the Y to the x-axis on the gshield the machine moved in the Y direction whereas the Y axis driver did not move in the x direction.
When I disconnected I disconnected the 4 wires on the right side if you were facing the machine. I did however reconnect them prior to the test so both of the Y motors are confirmed working.
Your response said that, with the change, the X axis worked but the Y axis didnāt.
So, what you had was the Y axis (machine) hooked to the X axis (gShield) which would indicate that the problem didnāt move when you reversed the wires.
If the problem moved from the Y axis (machine) to the X axis (machine) then that would indicate a bad Y driver chip on the gShield.