You solved the problem while I was typing my reply, but I figured I would post
it anyway.
It is quite possible that there is a problem with earthing or grounding. That is
one of two common causes of communications issues. The other is electrical
noise injected into the power line or radiated through the air. The principal
source of noise is the spindle if it has brushes, or is powered by a VFD.
Sometimes an idle VFD or a switching power supply can generate enough
noise to cause problems. The PMDX-416 has a filter called a common mode
choke to block most noise at its USB input. Some computers have this, but
many do not. This is why you see some USB cables with a lump at the end.
That lump contains a common mode filter. We offer small common mode
filters (also called ferrite chokes) here:
http://www.pmdx.com/USB-ChokeGrounding problems are often the result of a "ground loop" where the ground
of the computer is not at the same potential as the ground of the controller.
This results in current flowing through the shield of the USB cable. Normally
this should not happen to a PMDX-416 because the inputs are opto-isolated.
Make sure that the GND at the PMDX-416 does not connect to the chassis
or safety ground at your controller. This could happen by the metal shell of
the USB connector rubbing against the chassis, or by a wired connection from
GND of the board to the chassis.
If the above does not cure the problem, then I would recommend that you
connect an 18 AWG wire from the chassis of your computer to the GND terminal
of either J2 or J8 on the PMDX-416.