do a search with the words "gearbox noise" and you'll uncover a load of threads...
Heres one I started for my problems...
http://www.mini2.com/forum/showthrea...=gearbox+noise
Incidentally, my gearbox flywheel and clutch were all replaced at the same time... at that point the dealer told me that Mini knew about it, but hadnt worked out a fix yet, its something to do with a tolerancing issue inside the box... mine sounded like a diesel...
If you let the clutch out really slowly whilst in neutral with the engine running you wont hear the noise, thats because the tolerancing problem doesnt get aggravated... It took me a long time to get my dealer to sort it, and wasnt very pleasant, but they did it and now its perfect !....
Good luck, for your reference my dealer is Prestonhall Mini in Stockton-on-Tees....