[StevenB]

Just to second what's been said already: if you've pulled out the PWM cable, and the motor is still running, the problem is the speed controller. It can't be the code, it can't be the encoders*, it can't be the computer, it can't be the joystick, or anything else. If there isn't any signal going into the Jaguar, and it's still running, it's broken.

I don't know what your replacement plan is, but you probably don't want to run one side of your drivetrain with a Victor and one side with a Jaguar. They have slightly different input/output curves, so the motors will run at different speeds given the same input. It certainly won't break anything, but it will probably be harder to make your robot drive straight.

* If you're using CAN, there is a way to run the Jaguars with direct encoder feedback, which will allow the Jaguar to drive the motor without being sent a constant command. Even so, it still shouldn't run on startup.