Hey,
had the exact same problem as you not so long ago. Same issue at the lights then brought to mechanic and told it was fine then went again. I too have a A3 99.

Bad news is that I ended up getting a new gear box(re conditioned) and changed the clutch aswell. Expensive operation especially as the guy who reconditioned a gearbox left a bolt loose, it fell off which broke a seal and all my oil poured out onto my driveway!

Best of luck with it.