I THINK I know what's going on but I can't tell for sure.
I have a light bar (like, emergency lights, not the white spotlight style) on my truck and I don't want any extra holes in the roof (one for the VHF/UHF is enough). I ran the wiring down the inside of the roof rack and then through the space in the top hinge. Recently instead of running it all the way down the side and under the truck to get it back in, I ran it through the vent at the top of the roof line.
I've been noticing that when I go through a car wash, water is now coming in above the top trim piece.
I can't see any active holes or rust anywhere in the rear, so I feel it HAS to be coming in through that vent (since the wire bundle for the warning lights are keeping those "flaps" behind the vent held open).