Q: After it has rained, my windows make a loud squeaking noise when they go up.
A: This has been reported by a few, and they took their cars into a dealer for a window regulator or motor to be replaced. You might also want to try Gummi-Pfledge, a BMW rubber care product. A 2.1 ounce tube part # 82 14 9 407 015 retails for $7.50. It protects and takes care of rubber items. It prevents door weatherstrips from freezing up in winter and keeps the rubber pliable. I cleaned the strips with Spray-Nine prior to appling. Although it comes with its own applicator, using my forefinger was the way to go. Applied sparingly as recommended, one tube should last for years.
Update: BMW is currently redesigning the rubber window molding, it should be released in the first half of 2002, I'll post another followup as new is released.
Source:
http://members.roadfly.com/loki/e46m3_faq.html