I think I may have the same issue and I'm eager to know what's causing it.
On bringing the clutch up to and on the biting point there is a small knocking sound, which lasts for the length of time the clutch is on the biting point (a second, maybe less!). It doesn't happen when the engine is off, but it's been there for about 8 months now and has started to get really annoying. It hasn't got worse, which is even more confusing, just frustrating that I don't know what it is!
I had it looked at last week and it's not the engine mounting points, and they mentioned it could be the gearbox which I really hope it isn't. It's almost done 53000 and it's a 2004 reg Mini.
Any advice or answers would be gladly appreciated