[Alan Anderson]

Noise on a PWM control line can -- and often will -- be interpreted by a speed controller as a throttle command. Normally the impedance of the PWM output of the controller is low enough that noise is not a problem. If something is not quite right with the driver and/or pullup resistor on the problematic PWM channel, the cable might be picking up random impulses that the speed controller reacts to by turning on.

I know it's getting kind of late to do any sort of experimentation, but if you can verify that using PWM1 can reproduce the problem, you might want to ask if NI would like to have it back for analysis.