I bought my Rubi with dual top and didn't know I had those panels on wrong until I picked up the Jeep after getting the 2 soft top TSB's done. It looked a way lot better after the service guys reinstalled those panels. Now after reading this thread I'll have a better Idea of what I did wrong.
Now if I can figure out how and why they broke and replaced one of the reardoor window frames.....

 

This link and the pics are the best at showing the solution. I took care of mine yesterday

 

wow. thanks so much for this thread. I have been bummed for the last few weeks thinking we had to deal with the flapping in the winter.

 

I did the exact same thing. If you install them right, it should be difficult to zip it up properly the first time.

 

I wanna thank everyone that helped out on this thread since I've been driving with that little piece of the window sticking out and flapping for 2 months. I knew it had to be folded into a slot somewhere but wasnt to sure about muscleling it in since I didnt wanna rip anything. Now i can finally wash my car without soakin the inside with soap

 

I just fixed them during lunch. great info. funny though, when I first looked at buying a jk, the one I test drove had the same problem, as the canvas would not stay in place on the passanger side, and I decided I didn't want the jeep because of this. LOL! I'm starting to think I may never want to bring my jeep back the to dealership for service. From what I'm reading, I think I may just sharpen my tools and go at it myself.