Yeah I had the same prob and I figured it out. When you close the door, it dosent happen everytime but you will notice that your window dose now seat fully into the molding. Witch leaves a hair slit crack. An water comes in through there. So the reeason is that the molding is getting worn out. I got to change mine. Wat I have been doing in give the window a push after I close the door an that seemed to help me. But I'm 100% that is what it is.

The reason why the sealent didn't work is cause the waters coming through a slit between the window and the molding. Next time you shut the door. Shut it with maby a lil less then norm to make repeat the problem an ushould see that the window rests above the molding. I have the same prob