Rotator seems confused

I am trying to get my rotator calibrated for my observatory. I am using in an Exploradome, so I had to modify the gear size in the driver. Once I did that I thought all was well. when I tell it to goto 180 degrees it rotates perfectly to exactly 180 degrees south. Same way for north where I park it. But when it tries to synch with scope the dome is 180 degrees off. Then I tried making it goto 90 degrees, instead it went to 270 degrees. So it seems like it thinks it’s in the Southern Hemisphere or something. I wonder if there is some parameter in the set up that I have over looked. Also the dome rotates counterclockwise to find home rather than clockwise which the documentation says is how it is supposed to work. This is with the arduino version of the Nexdome driver. My magnet is at azimuth 1 degree, and north at 6 degree.