Scratch that. My curiosity was killing me, so I went to see what switch was being made. Found these photodetectors" on either side of the front of the roof opening. My glasses were breaking the beam! Now, if I could only figure out what the purpose of these were...
...well, I do know the moon roof closes automatically when the car is turned off. It must be there to determine if somebody's body parts are in the way of the closing panel.
You mentioned that "it's no longer smooth". Does that mean it was smooth when you first got it? Really, the only thing that could effect it is the tire preasure, as navigator3740 said, or the shocks. Is it possible somebody replaced the shocks?