That sounds to me like a programming issue, not electrical. But either way, here's the steps i would take to try and debug it:
1. double check the wiring, since this is quick and easy:
- Is the cable between the cRio and the Digital Sidecar fully inserted on both ends?
- Is the PWM cable correctly attached to the PWM outputs on the Digital Sidecar?
- Is power being supplied to the Digital Sidecar properly?
- Ensure there is NO jumper on the pins next to the PWM port you're using.
2. Check the code:
- What slot and channel is the code set up to use? Is this the correct slot and channel? (Slot - the position on the cRio the Digital Sidecar is connected to; Channel - the port number the PWM cable is connected to)
- Are you using the Jaguar class provided by the FIRST libraries?
If that doesn't help, i would go back to the basics. Run through chapter 2 here:
http://usfirst.org/roboticsprograms/....aspx?id=10934
The getting started guide has you load some default code, hook up joysticks and jaguars and ensures that everything works (you should see the Jaguars respond to the joysticks). From that, you can be sure the wiring is correct, and compare the default code with yours to find any programming mistakes.