Does your car have sunroof? I have this same problem on my 1994 SLE. I pulled the carpet aside (I was just getting out of my car after 50 mile drive in heavy rain) and it didn't look like it was coming from around the door seal (no run marks in the dust), but the wetness was all at the door side of the drivers floor extending in to the middle.
Yes my car has a sunroof. I took it to a different dealer today. They said they found the problem there is a water deflector that keeps the water from going inside. They had to order the part. I will keep you updated.
I actually had to take it back today for the same problem on the same door the dealership "fixed" a couple of months ago. There is a service bulletine for it I think the number is PI#101009. I hope they got it this time.