[Al Skierkiewicz]

Tom,
Both the Jaguar and Victor switch the same way. There is no -12 volt output. Both simply connect the negative lead of the power supply to one or the other of the output leads as direction command dictates. The switching on the Victors is speced as 120 Hz while the Jags are speced at 15kHz. If you were reading a very small amount of 15kHz energy when the motor was not turning but your finger helping the motor returned output to normal I think you have another problem. I will bet a buck that in both motors you have one shorted winding. Every once in a while, the motor gets on the shorted winding and shorts the output. (or the motor is resting on a good winding next to the shorted winding) Your conveniently placed finger moves the motor armature to the next segment and the motor starts to spin on it's own because the motor is able to rotate past the dead winding. Herein lies the rub, the jags have a current sense that holds down the output in the event of a high current or a short. If the short lasts for a certain length of time, the Jag goes into fault condition and turns the LED to red while disabling the output for 3-4 seconds. You may have also noted that the Jag always has a small pulse added to the output even when at full throttle. This is required because the charge pump used to turn on the FET gates needs to be charged. As Mike and others have discussed, the PTC is in series with the motor but no filtering for RFI is shown in the documents. Additionally, please check that the motor does not have a short to case. If so, you may have a sneak path through other devices (most notably the Crio and camera) that are interfering as well.
As to why the Victors always work, I suspect that you just haven't tried enough tests yet. There is very little reason for a Victor to work in this application when a Jag does not. Although the inductance of some KOP motors is high enough to change the output waveform of the Jag, the impedance/inductance of the window motor should be small in comparison.
The singing your students hear is the laminations in the motor moving at 15kHz.