That is EXACTLY what happened to me! Stealth Racing replaced my worn discs with genuine Audi discs (I hadn't been getting brake reaction before then, from what I remember) Then after a short time, I got heavy judder when braking. So they replaced those discs under warranty. Same thing happened, so this time Stealth replaced the discs with Brembo units this time. Again, after a while, the judder was back! Boy, was I gutted! So A2 cars had the discs skimmed and fitted a new wheel-bearing. I'm not sure if the bearing was actually faulty or if it had not been aligned properly. I do know that that alignment is critical, though. Anyway, since then it's been totally cured! So I'd be fairly sure that your problem does lie with something to do with the wheel bearing? I hope that this helps ..
David