I had a problem with the pass through window on mine. It is pretty much useless, so I put a piece of black Gorilla tape down the joint onto both sides of the joint, and I haven't had any water come in there since. It means the window can't be opened, but how many times have you used that window?
The other thing that we do when travelling in the rain or dust is to keep the roof vents closed. I have Maxx Air vent covers on both and the aerodynamics want to create a vacuum in the camper, so water and dust come in all the little gaps.
Brian