I had a 2003 Mk4 GTI box here that broke the thrust washer behind the pinion. It was noisy in all gears. Parts were cheap but it was labour intensive. The second gear syncro is a 2 piece unit and not usually a problem. Until it is disassembled it is hard to say what your problem is. I would be suspicious of the thrust washer, which is the same washer as in most of the other boxes.
golflaki, the rivets going in the DUU 1.6 boxes are a very common problem. By the sounds of it, you were lucky as 99% of the time they poke a hole in the housing and stop!!!!
Cheers, and good luck with it,
Andrew
Par 6 Golf GTI. Coilovers, BBS CH Wheels, APR'd
Caddy van 05/07 (colourcoded) (BRIGHT! orange!) coilovers, Konis 18in. wheels, Oettinger tuned
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