Its most likely the drain hole on the door. water is entering the door via the glass wipers and running inside the door. There are small vents at the bottom which if blocked will cause the water to rise abve the seal.
If that is not the cause check that the bungs on the floor panel are still flexible.
Also check that the door is closing against the rubber. You can adjust the door clamp a little to adjust this.
mike, August 2007