[Mark McLeod]

So you have two distinct problems.
Although your question is about the second problem, I don't expect your recoding of the Joystick to do you much good until you've resolved the first issue of the unresponsive motor controller.

From your testing of the motor controller in the PWM port that works, it sounds like the motor controllers are fine and the PWM cables are plugged into them properly.

Which PWM port works?
When the non-working PWM port is connected, what is the motor controller status light doing?
Are the three green power lights on the Digital Sidecar all brightly lit?


For the addition of the Joystick you might want to post your Begin.vi and Teleop.vi, so we can see if anything's not hooked up right. But the PWM port won't suddenly start working because a new joystick was added.