My puddle has never been on the floor mat though, it has always been under it. I presumed that the water was coming up from beneath the car or dripping down along the floorpan of the car.
I had this exact problem - it's the vapor barrier in the door.
If you take off the door panel, there you'll find a gray piece of foam-like material. It's attached to the metal door with a bead of sticky rubbery "glue". The glue doesn't stick so well, and near the bottom of the door especially, it lets water drip in.
Usually this will occur in heavy rain when you've been driving a lot or at higher speed. The front tires kick the water up and it leaks in between the bottom of the door and on top of the door sill.
Check this out - I'm sure you'll find this is it if your carpet is wet under the floor mat.
I had this problem on the driver's door - fixed under warranty. Now my passenger door does it, but I can fix it myself. It hasn't mattered in a while - no rain and the 'Tour is in storage for another week.
Good luck.
Kerry