I "think" water, chemicals and substances can soak into the paint or coatings and leave stains/marks below the surface. I'd take the opinion of someone more knowledgeable on paint over mine.
Windows can have coatings on their surface, so perhaps stains that stay on the windows are stains in the coatings on the windows?
I 2nd the idea of polishing compound? The only thing you have to loose is a couple bucks for the supplies and a couple of hours of sweat rubbing it on and buffing it off. You should be able to find polishing compound anywhere where they sell car wax. There is coarse and fine, be careful if you use coarse, if you rub to hard on badly damaged paint, it can right through it. I doubt your paint is that badly damaged.
Another option, something I'm considering, WRAP IT. Youtube Vinyl Wrapping a Car. The supplies would only cost a couple hundred dollars, and it is something most DIY'ers can do. I'm considering doing my Commander in Matte Military Green.
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Last edited by Mongo; 10-02-2013 at 10:03 AM.