[Brian C]

While I admit to being more familiar with Victors than Jaguars the controller may need to be calibrated. This is the procedure directly from Luminary Micro's information:

CALIBRATION
PROCEDURE
To calibrate the servo-style PWM input for a
specific range, connect a PWM source, then:
1. Hold down the USER switch with a
straightened paperclip.
2. After 5 seconds, the LED flashes Red and
Green to indicate Calibration mode.
3. Instruct the controller to send a full-forward
signal.
4. Instruct the controller to send a full-reverse
signal.
5. Instruct the controller to return to a neutral
signal.
6. The LED will flash Green and Yellow to
indicate a successful calibration.
7. Release the USER switch.
The MDL-BDC samples these signals and centers
the speed range and neutral position between
these limits. A calibration failure will be signaled if
an out-of-range signal is detected.

Or if you're looking to have a motor go in an opposite direction from the joystick input as in tank drive where one motor needs to be in reverse when driving in one direction. You can simply reverse the wires on the M+ and M- terminals from the motor.