I took some pictures of this today. The dealer will be looking at my vehicle next week. This is one of six things I have asked them to address. This one really annoys me because I have discovered that the glass is misaligned and has scratched away the paint on my car. Lovely!
This picture is with the glass up. It has put a scratch on the inside of the tailgate frame. Sorry for the poor quality. It is covered in salt.
This is a picture of the bottom left corner of the flipper window and frame. As you can see it right next to the frame. There is a huge gap on the bottom right hand corner. The noise I have been hearing is the corner of the window bumping into the door pillar over bumps and high vibration roads.