I have a 2000 Mustang GT and my passenger side window seems to roll up too far and it barely hits the top of the window frame which causes it to have a gap. Its hard to explain so I made a video. YouTube - 2000 Mustang GT window issues
Perhaps the window regulator mounting positions need to be adjusted. I'm trying to picture this in my head and I would think that if the front of the window was a little higher than the back of the window, then the back would be off of the weather stripping because the front is sitting too far up on top of the weather stripping up front. I think it lines up when you roll the window up when the door is closed because the front of the window goes into the right position under the weather stripping and thus it doesn't cause the whole window to be off position. Hopefully that's clear enough for you to picture in your mind.
Edit: Looking at the video again, it could be the back of the window that's too high. Not sure. Either way, I would look at the mounts for the regulator.
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