With nothing hooked up you stil get a short indication between motor #1 and ground?
That isn't a ground issue.
It sounds more like a problem with the controller itself.
Can you disconnect the wires at the controller again, Then, while probing the controller itself, find the ground connection and with nothing connected, probe between each of the other connections and the ground connection?
If that then shows a short to ground between the #1 motor and the controllers ground, It will mean the controller is shorted internally.