For what it's worth on my 06 limited coupe when doing a fine cut polish on the clear coat, I noticed that the rubber seal for the rear passenger quarter window was not positioned correctly. The body radius is quite pronounced where the seal interfaces , and my seal was laying on top of this radius, it looked supisious so I looked at the driver side. This seal was neatly rolled toward the downward side of the body window radius , thus keeping the seal tight and any water that contacts the seal has to stay on the outside and not work its way under the seal. It was easy to fix, using my thum finger nail starting from one end I gently pushed the seal down and in.
Hope this helps someone
Cheers
Mongoose57