josh,
That's pretty unusual as green and blue is not an error code we have programmed into the VorTech controllers. That said, I would try to perform a hard reset on the controller by following the steps below:
1) With the controller powered on, press and hold the "Mode" and Set" buttons until the dial blinks Red, White and Blue.
2) Press and hold the "Mode" button until dial blinks Red and Purple.
3) Press and Hold the "Mode" and "Power/Option" buttons until the pump powers off and resets.
Please contact us directly if you continue to have issues.