Ok I fixed it. Seems you have to reteach the position of the sunroof.I followed this procedure and it closes all the now.
Sunroof not closing flush with the roof?
If you notice that when you close your sunroof, that it is not closing to the proper position; either too high or too low, so as not to seal correctly, you can use this fix to recalibrate the sunroof closed position.
This is from a TSB from 2005. Steps 1 throug 6 concern reprogramming the sunroof module with Starscan (deleted). You can do steps 7 through 12 in your driveway right now. I did and saved myself $675 at the dealership.
7. Place the ignition switch in RUN position.
8. Close all of the doors.
9. Press and release the vent switch (sunroof should move to vent position).
10. Once the sunroof has stopped motion at the vent position, press and hold the vent switch
for at least 5 seconds to recalibrate the sunroof position.
11. If the sunroof did not reach the full vent open position, press and hold the vent switch until
the full-vent-open position is reached then release the vent switch, then press and hold the
vent switch for at least 5 seconds to recalibrate the sunroof position.
12. Cycle the sunroof from the full-vent-open position to the full-slide-open position and back to
the full-vent-open position at least 7 complete times. The sunroof is now in customer mode
with the obstacle detection thresholds updated.