I'm assuming you have followed the directions carefully for installation and calibration on p8 of the manual.
The position sensing pot in the HyGain rotors is a bit unusual because the wiper is at ground potential and the ends float relative to ground. I would suspect that something is wrong in this area of the circuit. Check resistance to ground of your rotator with the control box disconnected, as per the HyGain rotator manual. This is from pin3 to pin1(ground) and pin7 and pin1. The sum of the two resistances should be ~500 ohms and the ratio should roughly correspond to the antenna position (i.e. if they are equal it is due north, assuming a north centered installation). If this checks out, look for errors in the wiring or circuit board for the position pot connections (R1,R2,R3,C1-3,D1-2, or the corresponding components for 'A' on the schematic/board.
Another test is to disconnect terminals 3 and 7 to the rotator and hook up a 500 ohm pot to terminals 1/3/7 of the controller. Leave terminal 1 connected. Do not make any movements or commands, but as you turn the pot the needle should respond and move through the entire 360 degree range.
I've built 3 of these with no issues.
GL,
-Tony, K1KP