Okay, I have a 1999 National Tradewinds that has a rubber roof that does the same thing. Solution for the windshield was to get a gutter like product that keeps the streaks off the windshield. The side windows still need to be cleaned from time to time and I plan to overcoat the top this next spring. Hopefully that will solve the window problem. I think I got the windshield gutter material from PPL out of Houston.
Hope this helps. Arnold