I got the same problem, on the rear hatch I'm going to try silicon on the side edges where the end of the taillight meets the body. I figure it will trap the water even as its going up and any over flow will fall out when the gate is closed .
As for the windows I think it's the rubber strips have some type of felt sound insulation and that is soaking up and holding the water, only to release it as the window rubs on the way up. The price we pay for a quiet ride