Did you clean out the discharge port? For mine, black dirt clogged the port but it didn't looked plugged because of the color. It was only when I put my finger up the opening that I found all the dirt; water slowly washes the dirt to the port over time but doesn't have enough pressure to force it out. Eventually the dirt builds up to plug the discharge port...Ran my '09 TC through an automatic carwash yesterday and lo and behold I had a wet carpet on the back passenger side when I pulled around and started to vacuum the interior. Stopped by Lowe's today and bought a length of rubber marine and auto seal with the self adhesive tape on the back. Took apart the cowl and there was a section of the factory seal that had just disintegrated and was completely missing. The hardest part was removing the sticky tape and glue residue. A little heat from my heat gun was all that was needed though and it came off with a little elbow grease. Cleaned it all up with a little isopropyl alcohol and applied the seal making sure to leave no gap between the points where it joined. Got everything all back together and fired up my pressure washer and purposely blew water all around the cowl area. No water made it through.
Also to note: I bought a bottle of Concrobium mold remover and preventative and soaked the back seat carpet and let it sit for a few minutes before using a towel to dry it up. Hopefully that will ward off any mold growth from starting.
This is the weather strip I purchased and used. Installation was easy and it is very flexible.