I have the same problem. So far as I know it happened only one time. That was last Friday (December 18, 2009) We were out in a very hard rain. The car was sitting most of the time when it rained very hard.
A friend was riding in the back seat and he noticed the wet floor mat and carpet. I was using the air conditioner part of the time that day and was concerned that I might have some water coming from the AC.
I just visually checked the door seal and found nothing. It seems to me that the seats would have been wet in addition to the floor if water came in through the door seal.
If anyone has suggestions please let me know. I have a 2004 Town Car.