Passenger's Side Window Does Not Close Properly - Help!

[Boxtah]

Hi, I recently noticed rain water coming into the cabin of my '02 986 Boxster S from the passenger's side window. It turns out that when I open and close the passenger door, with the windows up, the top edge of the glass does not seal with the roof correctly. I'm guess it's not dropping or raising a crack, like it should, for air-pressure release, when I'm opening / closing the door.

I simply do this to fix the problem: Lower the window and close it again, when the door is closed. When I do this, the top of the glass seals properly with the roof, and nothing leaks. But if I open the door with the window up, and simply shut it, the window won't seal right. Essentially, every time that I open the close the passenger's door, I have to manually lower and raise its window for it to seal right. Interesting, when this manual process happens, I hear a slight clunk in my door panel, as if something was not catching before, and now is caught and aligned.

Has this happened to anyone? What is the culprit, and the fix?

Thanks!