[Al Skierkiewicz]

Justin,
Although the change in color is not explained by what I am about to tell you, remember that the motor itself has a thermal cutout internal to the motor.
The next step is to place a VOM on the input terminals of the Victor to insure you have a solid 12 volts at this point when the motor is under load.
I would also try running the default code for that motor (all others disabled) and see if in fact the code has a problem. I believe the LED is telling you that the PWM is changing but I don't know how the Victor reacts to bad power under load. The best method to find the problem is to eliminate all the variables.