I have. 2013 JKU and have noticed that the narrow flap on the leading edge of the side windows don't always seat as well as you think they should. Often the top and or bottom is only partially engaged in the door. Am I doing it wrong? Any tips would be appreciated.

 

New soft tops are stiff and hard to work with.

My install method;

I start the zipper (an inch)
Then Insert the forward edge into the door surround (the plastic thing)
Next Insert the bottom edge starting at the front and working back

I then grab with both hands the very back edge of the window and pull backwards (This helps align the window)
I go back the the leading edge and make sure it's completely seated in the door surround channel again.
Then I zip it up and Velcro it down.

They do get easier with time.

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That is exactly how I have been doing it. Just wanted to make sure I wasn't missing an important step in the process. The worst instance was this past weekend I had to remove the back window to haul a twin mattress. The lack of tension from removing the back window made the passenger side window leading edge come completely out. I put it back in place an pulled the window toward the back and it was fine then. I guess it just takes practice.