I took some pics of mine.
See pic: PA181446comp.JPG - File Shared from Box.net - Free Online File Storage
The two rubber bits should rub each other and seal at points marked A and B. See how mine obviously touches (because it is clean where they touch.)
Best way to fill that gap would be a small piece of self-stick weatherstrip stuck on where I marked A or B. (Obviosuly clean the surface well first.)
BUT - I bet that's not where it leaks. The top molding makes a little ledge where I marked C. The water puddles on this ledge, then runs behind the weatherstrip that goes around the perimeter of the window opening. I had leaks there on both sides. A little silicone (RTV) applied right at the bottom of that ledge against the edge of the seal (where I marked C) will stop the water from getting through the little gap and force it run out the back like it's supposed to.