I found that the front door (2dr) membrane and outer door seal was the culprit on mine. When I removed the membrane to do the dynamat i noticed the rear floor was drenched after a spot of rain, so as soon as I could I replaced the seal and the membrane in a one'r. I also removed the door handle and whacked a load of silicone sealer behind it, as it was coming in through there in torrential rain.
The door seal was £15 from VW, abd the membrane was a sheet of plastic I found in work, fixed to the door with tank tape. One tell-tale sign is that the bottom edge of your door panel (right hand side of the o/s panel) is slightly damp or showing signs of damp.
Hope this helps?