I collected a bunch of controller data over the serial port on my laptop and sent that off to Azure Dynamics for analysis. After looking at the data, the ISR2Hertz variable (i.e. RPM) was pegged at zero. This led me to believe that there was something wrong with the motor encoders.
I opened up the motor speed monitor box and probed around. All the encoder signals were up at 4.9 volts and the black ground wire was also up around 4.83 volts. After examining things some more, I found a broken wire on the AMP connector going into the controller.
Here is the black broken ground wire. I'm not great at fixing these things, but I'll definitely give it a shot. Worst case, I can get one of the technicians back at HP to help me fix it.
I let Azure Dynamics know so they don't spend too much time on the analysis.
Next Up: Try, try again...