and as I think about it.. I don't think the back window panel could stretch outta shape that much as to be an issue... maybe bring it in to dealer and have them look at it
I can't speak for you, but I have driven on hwy with roof back and back window in. Mine hasn't loosened to the point of flapping or to be an issue. Some folks have had to adjust their front latches due to being loose. I assume you don't have any issues there...
good question... tho I had driven jeeps since the late 70's... I think the bug finally got me in 1987...my first jeep... a YJ with the square headlights.
some movement is normal.. hard to tell about your situation. I have run mine with window in and bottom channel not connected.. slightly more movement but not floppy