I have a Leer topper on my '09 Silverado. Absolutely no leaks.
I believe '9 was the first year that GM made the edge cover of the tailgate with a nose on it. I did not like it, was told that the bottom edge of the topper back window would sit on top of it. So I had it replaced with the previous style that fits flush over the edge of the tailgate. So the rubber flap attached to the window hangs over the edge of the tailgate.
Not knowing which style you have, maybe there is your problem.
I also installed foam tape to close the gap between tailgate and the sides , but that was more to keep the dust out.
Alex
