Almost always the moister seal INSIDE the door.
If you checked the rubber seal around the door body fitment that is usually fine.
Every scirocco I have owned (counting over 15 now) has had that seal either removed, destroyed by someone putting in big speakers or just gone hard and cracked.
Take the door card off and look at the plastic moisture seal. It needs to be intact and sealed around the edges. Usually they are not
You can buy a new one from VW. OR get some heavy duty mac-tac (that peal and stick stuff) that you can stick on the door and then use a hair dryer to shrink it nice and tight.
All else fails you can get some poly from home-depot, etc and silicone it on. but that usually only last a year or so as the silicone usually starts to leak.
If that is the culprit then also check your window scrapers, if they are going bad (shrunken and hard with age) they will let more water into your door than normal.
Lastly, if you have the seal off. Clean out the bottom of the door, as all that water will leave a nice sludge in there. There are supposed to be a couple drain holes in the bottom of the door that lets the water out, and these ususally get clogged over the last 20 years of your cars life
Good luck and keep us posted.
Leaky A1's seem to be common around here.....