[Astronouth7303]

Are you sure the RC is reading the sensors correctly?

What I did to test our GTS's last year was put the last 4 PWMs in User_CCP mode (digital outputs should work equally well) and have the interrupt handler toggle that. I then hooked an oscilloscope to both the GTS and the CCP pin. The wave forms matched nearly perfectly.

In terms of software, the GTS and encoders should be very similar, ignoring direction. Even just putting an LED on the output pin and watching its apparent brightness should be helpful. (You probably won't see flickering, as it goes too fast.)

If that works, you may need to post your code so that we can look at it.