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I have never had this problem with my Boxster, but I had a similar experience with my daily driver a BMW 5 series. I had a lot of water in the rear passenger foot well behind the front passenger seat. It turned out that there is a vapor barrier inside the door and when it rained heavily the water ran down between the window and the door as it's supposed to, but instead of following the drains in the bottom of the door back out it leaked into the back seat area. Put in a new vapor barrier membrane and problem solved.
I don't know for sure but I bet Porsche uses a similar vapor/water barrier inside the Boxster door. That may be the real source of your leak. Take off the inside door trim and check it out.
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