I dicovered a rear window leak on my 2010 access cab around Christmas. On this forum I found a TSB regarding the third brake light leaking and issues with the window seal so I took the truck into the dealer, after 3.5 hours of waiting around I was told that a. the problem would not be warenteed and b. they couldn't determine what the cause was because my canopy would need to be removed.
Angry, I took the truck to Speedy Auto glass (who slide the canopy back for me) re and re the rear window to discover the window was NOT glued in. (see pictures) there was a small section on the drivers side which had a 12' piece of glue and that was it. Water had likely been pouring in through the gap for ages I just never noticed.
I returned to Toyota dealer with my reciept from Speedy and complained to the service manager. He of course told me that I no longer had warentee and it was out of his hands. After a month of waiting I was told Toyota would re-emburse me half the cost of the window.. what a joke!
If you are having water problems in your rear window, find out if they glued the thing in!