Is the calibration on your compass off by 180 degrees? If you've replaced the top cover on your dash, it's possible that the compass got put onto the new top cover backwards. I know for a fact that the compass module will fit backwards with no problem at all.
This guy that I know....yeah....a guy I know....he re-installed the compass backwards when he swapped out the dash cover on his JK. Yeah. It was just a guy I know. No way it was me.
Good news is that it's a VERY easy fix. If you installed the new dash cover the first time, I'm positive that you can figure out how to flip the compass module around the right way.