I had this same leak on a 98 3500 1 ton. It was brand new at the time and I took it back to the dealer 4 times and it still leaked after each time. They changed door seals and carpet 3 times. Finally I asked the service manager if the body shop had done the previous repairs or was it some mechanic. He said the body shop had not been involved so I requested they check it out. Turns out the cab seams were never sealed from when the truck was built at the factory, (the thick bead of putty place over the welded seams).