There is also a seal that the window sits in and kinda seals against the bottom of the window opening when the window is up. Think it just keeps bigger debris from going down in the door Its #6 lower window seal runs across the bottom of the window.
http://www.lmctruck.com/icatalog/ca/full.aspx?Page=19
I had a long piece of hardened rubber laying at the bottom of my doors , took me a little while to figure out that they were the lower seal that had fallen off.