Kind of sounds like you have a grease film left behind.
How did you install the window and rubber seal, WD-40, go-jo hand cleaner, Dawn Dishsoap, silicone spray?
We used to install Peterbilt windshields and the rubber zipper lock with Go-Joe hand cleaner. That left a nasty film behind. We first cleaned the window and rubber with a fast dry enamel reducer (Dupont 3812), I imagine a wax and grease remover pre paint product would work too.
Then we would follow up with Windex and paper towels, changing the paper towels often. Doing the cleaning process twice with the Windex.
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