I had a similar problem with my mk5 gt tdi which was driving me crazy. After much searching on the net i found the water was getting in through the boot flap...
There is a small flap on the right side behind the bumper that allows the air to flow out of the boot when you shut it. You will need to take the rear bumper off but its really easy. I just took it out and resealed it with silicon and have had no water in the boot since.
Heres a pic of a mk4 its in the same place