Does your antenna move in both directions? If yes, please continue.
Input 000 with your remote. Your antenna should be pointing north when it stops. The Rotator should be on the North side of the lower mast.
If these are not as described, then it must be corrected.
Input 090. Your antenna should point East. It should be turning Clockwise (CW) from 000 to 090. That is clockwise, from over head, birds eye view.
Whenever the controller is counting up, the rotator needs to be turning clockwise.
Whenever it is counting down, it will be turning counter clockwise. (CCW)
If it is turning in the opposite direction of what it is supposed to be, (CW vs CCW) then 1 and 2 are likely switched.
If you continue to experience issues, I highly recommend that you double check your wiring.
It does not matter what color wire goes to any terminal. #1 on the controller must go to #1 on the Rotator. Same with 2 & 2. 3 & 3.
If you are unable to check your wiring, I'm happy to test your controller.