Hey rhyso
I have gt tdi 130bhp 2002 and when i first got the car this year it done a simliar thing but this was everytime from cold, as i work at a vw/audi dealer i got it checked out and it needed a updated ecu the new ecu had updated software in it, so i took extended warranty and got a few other bits done, it did cure the problem, i would get it checked out at a dealer or someone who has a computer and can read fault codes, there is something out via vw on ther elsa machine which says when you put your foot down on the clutch the noise/vibration goes try that and if it goes then it could well be the engine ecu i am afraid