I have the same thing and I have tracked mine down to the seamsealer around the seams at the top of the window and in the lip around the roof. My metal isn't rusted just the sealer is dried up and has shrunk to where I can see cracks in it. I am kind of wondering what would be a good caulk to use to get it sealed up. I am wanting to put new carpet or rubber mat in and don't want the rotten smeel of wet backing all the time. Also check your windshield gasket.