[Al Skierkiewicz]

Ted,
You are describing several different problems. As pointed out above, the DSC could have power issues, the multi pin connector could be loose or the Jaguar could be in protect mode. In the latter, the LED comes on red for 3-4 seconds while the output is disabled. Protect mode can occur due to high temps, high current, low power supply or limit switch jumper is open. It is also possible that you have metal flakes down inside the Jaguar.
You do not indicate that you are running PWM or CAN so a loose PWM connector can have similar issues. There is no LED on the Jaguar that flashes orange/yellow. There is a red/yellow flash that indicates a failure in the calibration mode.