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My old 87 T-Bird did that back in the day. It appeared that the felt lining had rubbed off the rubber strip and now it was rubber contacting the glass that caused the problem.
I fixed it by gluing some black felt material to the rubber there and it was all set.
The other problem was that it was causing the window to bind on the way down since the rubber was gripping it.
You will have to figure out the root cause before you can come up with a solution, though.