I think I have an old Radio Shack version of this unit- the control has a large knob on the top, and when you turn the knob an internal motor runs and causes the disk with the indicator dot to move till it lines up with the selected pointer position. If this is similar to your rotator, there is one other thing that may cause alignment problems.
I found one of the gears in the gear train between the motor and indicator disk in the control box was made of a very low-grade plastic, which after a number of years turned into the consistency of dried soap. In my unit, one of the teeth broke off, causing the indicator to skip and hang-up from time to time. Eventually, all the teeth finally broke off. I removed the gear in question, and the plastic was so deteriorated you could snap it in half with very little effort using just mild finger pressure!
Try doing the calibration listed in previous posts by rotating the antenna all the way one way, then all the way the other way. While doing the calibration, watch the dial with the position dot on it. If it does not rotate smoothly, or hangs up from time to time, chances are one or more of the gear teeth in the control box are bad.
My rotator turns a small TV antenna located in the attic, which obviously has no wind load to deal with. Luckily, my rotator is pretty consistent, and takes exactly 60 seconds to rotate 360 degrees. I ended up using it manually- rotate it to one stop (I can hear the sound of the motor change when the rotator motor stalls), and use the second hand on my watch to time the rotator. In fact, if you run the rotator to the stop counter clock wise, wait till the second hand gets to 12 o'clock, and start rotation- then the second hand becomes a pretty good compass indicator as to where the antenna is pointing!
Yeah, it's a pretty stupid way to turn the antenna, but it will do for now, as it will be replaced by the HD-73 currently on my tower sometime this year when I upgrade that unit.
Good luck, de Tom, KA1MDAwww.ka1mda.org