I tested a bunch of PCBs -- Samsung, Hitachi, WD and Seagate. As expected, none had shorts between any motor phase and ground. A genuine short would mean that the motor controller is bad. Clearly your board does not have a real short.

I suggest you retest the PCB tomorrow. Perhaps there is residual voltage on the gate capacitances of the low-side MOSFET drivers which is responsible for the false readings. In fact that's how you would test a discrete MOSFET with your multimeter -- charge up the gate and then measure the resistance between drain and source.

_________________
A backup a day keeps DR away.