I just finished a long-running battle with water in the trunk. Part of the problem was a leaking window gasket. The water from the lower driver's corner of the rear window ran into the speaker depression on the rear window shelf and dripped out the speaker wire hole and into the trunk. It was also intermittent and depended on the amount of water in the depression as well. I replaced the seal and used silicone sealer in the window channel of the seal as well as around the metal window opening.

The main leak was around the trunk seal. I removed the seal, cleaned and painted the seal channel and replaced the seal with a new one using 3M black weatherstripping glue. I still had the leaking. I had installed the seal just like the old one, but it did not "look" right to me. I even checked out another vehicle and it too had the seal installed the same way. On a whim (and also as a last resort) I removed the seal and cleaned out the channel again. I reinstalled it in reverse fashion and voila, the leaks ended. I also used permatex black silicone rather than weatherstripping glue.

I don't know if I can describe the installation, but I installed the seal with the "tall" side (the side which contacts the trunk lid) towards the inside of the trunk. The seal now forms a channel for the water toward the outside of the trunk. If you can visualize a cross-section of the seal, it resembles a "J". The "hook" of the "J" is facing toward the outside of the trunk. Also there is a small bump or bead on the "tall" side of the "J". This bead fits exactly at the top of the inside lip of the channel on the inside of the trunk. This leads me to believe this is the correct installation rather than the way the original seal was installed. Also, I'm not sure the seal in the car was the original seal (same with the other car I looked at as an example).

The seal will fit either way, but this way solved my leaks. It also made the trunk lid harder to shut (similar to the doors when new seals are installed.