Hi emb110,
Where are you getting your information/numbers? I set the AP heading to 90 and saw 88 in the TRK MAG box in the moving map. But I also had a little bit of wind. Track and heading are not the same, so this is to be expected.
Track is your actual route on the ground, and heading is where the nose is pointed. If there is a cross wind you can drift. You'll need to look at an actual heading instrument like the HSI.