The Jaguar by default uses a longer PWM pulse then the IFI control system or the VEX controller puts out. This means that it will work, but the fastest a motor would go is 2/3 speed.
You can calibrate the PWM input on the Jaguar so that it will operate at full speed with IFI control system. See the Jaguar Getting Started Guide from
http://www.luminarymicro.com/jaguar
Be sure to calibrate it again when you go back to the cRIO.