[Al Skierkiewicz]

Daniel,
The lights indicate that you are not going to full throttle in each direction but that is usually the case. If the control fault is not software related, Jag calibration will match your controller to the full output of your joysticks.
If you are only testing the output of the Jag with a voltmeter, remember that the Jag output switching frequency is 15kHz which is way above the frequency limits for many voltmeters. They are also not intended to read PWM, square wave signals. The Victors are 150 Hz which is in the range for most meters but are still not accurate due to the square wave output of motor controllers.