I had this in my TT I recently sold and never got to the bottom of it annoyingly! I put it down to the new windscreen and got autoglass back out to fit a new one, even after they did a leak check which came back negative, they grudgingly did and a few days later it was happening again and I gave up.
Watching Fithgear last week he was showing how 10 year old merc footwell would start collecting water due to leaves falling down the windscreen and collecting in the bulkhead and rotting but could be fixed with a good clean!
That would of made sense to my TT as I parked it under trees all the time and I now park my GTI in a similar position I am going to be very wary about it happening again.
Worth a try!