Connecting the USB shield to earth gnd on your chassis creates what is called a "ground loop" and allows current to flow through the shield, including any electrical noise from your motors/spindle. This in turn can induce noise onto the USB signals inside the cable, or into the isolated side of the USB interface on the PMDX-424. So my answer is "don't do that".
It *is* interesting that apparently the PMDX-424 can communicate with the PC at least briefly.
Bob