On my 2004 SE7 I have water intruding at the back right passenger door after a washing. It appears that the top portion of window frame is not quite touching the rubber molding. I can push at that point and feel if it would fix the problem if I could adjust it in a 16th to an 8th of an inch. The lines on the lower door seem to be correct. Also that same door lock is not working so hope to get two birds with one stone when I open it up.
Kevin

 

Does the reset of the door alignment seem to match the rest of the body, if so the only adjustment is to, very carefully, bend the door frame, in slightly with your hand and some pressure. If done carefully, you can stop the leak, just do it slowly till it matches up.

 

And here is a TSB you might want to review as well, in case you fall in the impact range.

 

Savannah,

Thanks for finding this. My rear door had a leak and I guess this was it. I had to keep the luggage compartment cover on to catch the water while I tracked down the source. Luckily I had the right idea and put a bead of RTV on it. Thanks for the heads up, I have heard of a couple other with the same issue. Leak has stopped now.

 

There's always duct tape... available in camo and hot pink now....

 

I have the same problem with the rear driverside door. I got some A/C weatherstripping from home depot, and with a little Gorilla tape was able to seal it up. It was in the back corner, closest to the apline window. You could see where the windown frame did not press against the weatherstripping, and when i closed the door there was a little vibration in the window frame. You can adjust the windown frame, it's not welded to the door or anything. There's mention on the board somewhere on how it adjusts with a torx driver. Not sure if this will fix your problem. For me, my door is out of allignment, and I'm too lazy/poor to bring it somewhere to have fixed. The Gorilla tape is black, and you can't even tell its there. I read this as the passenger door being the problem, not the tailgate.