WOW, I wish I could have watched that video 6 months ago when my JK was new (my window popped loose more than once the first couple of times).You're doing it wrong. My guess is you're not inserting the L-shaped edge of the rear window inside the groove on the door surround. I've seen folks miss that. Check this video out. Pay particular attention at the 5:56 mark. Takes some practice, but trust me, the soft top is tight and shouldn't be flapping or coming undone.
Official Airpark 2010 JK soft top video - YouTube
Let us know how it works out.
Most of the comments above are probably correct, he might be doing it wrong, he might also have a bad window molding/channel. So, try reinstalling the window according to the video and also compare the two sides and make sure one of them doesn't look different (defect). Good luck and keep enjoying the JK.