A few months ago I noticed occasionally I was getting water on the front passenger floor. I could not determine the source of the water. Checked by the glovebox and it was dry. Today it rained and the floor was wet. I found the boot on the front passenger door, by the hinges, was not seated properly allowing water to enter the car through the opening. I think I reseated the boot properly.
Has anyone else had this problem?

 

This is all over the boards. Search is your friend. Here are a few to start.

https://www.chevyhhr.net/forums/problems-service-repairs-42/gallons-water-my-hhr-18093/
https://www.chevyhhr.net/forums/problems-service-repairs-42/wet-drivers-side-floor-anyone-18248/
https://www.chevyhhr.net/forums/problems-service-repairs-42/wet-floorboard-again-18237/
https://www.chevyhhr.net/forums/how-tutorial-library-21/fixed-my-water-leak-last-night-14263/

 

I knew about the butyl cover and the problems with the leaks caused by the sun roof. I didn't remember reading anything about the boot.