I have also had this problem. Everytime I put the window down in the rain, to grab a parking ticket for instance, water would be drawn up onto the inside of the glass. The dealer local to my office were next to useless, but thats another story. The dealer I bought my car from were much better. They replaced the window seals and this seems to have cured the problem.
Changing the seals has worked for the moment. There has been no water entering the inside of the glass as yet, but there will be plenty of rain to try with!
One idea to what created this problem is the seals became porus, ie lost their waterproofness. Everytime the window was raised and lowered it was squeezing the water on the inside of the glass.
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