Sun Roof
Sun Roof not closing Flush?
My wifes Jeep has had this same problem twice now. May be because she cuts the car off a lot while the sunroof is still moving. I’m just guessing.
Talked to the dealer and they said to bring it in and they would have to re-program it. I spent hours searching the internet and finally found a way to fix it without the dealer. So try this first and worst case, you have to go see them.
Problem: The sunroof glass will not close properly and is not flush with the roof of the vehicle. Will create wind noise and or water leak.
Cause: Sunroof  is Out of calibration
Resolution: (You will need a second person to help you with this. Unless you have really long arms.)
First, UNCALIBRATE THE SUNROOF.  To Flash & Reset. Place the ignition switch in RUN position. Locate the sunroof fuse (Mine was in the normal fuse box under the drivers panel (#2 -15A Blue) If you just pull on the panel under the steering column, remove it, this will help with the visual. (small pair of needle nose doesn’t hurt either) Now get your assistant to Open the sunroof and about 1/2 way, PULL the fuse  (while the sunroof is still in motion) Reinstall the sunroof fuse. Now, RECALIBRATE THE SUNROOF. Press and HOLD the sunroof vent switch until it stops at the full vent position. Verify sunroof operation by opening, closing, and venting the sunroof.
Details: If the above procedure is sucessful, have dealer reprogram/update the sunroof control module with new software  (So Far I have not had to do this) and it’s been a year.
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