You are the first person I have heard speak of the same problem I have!!
I have issues with my 06 mini one. Kangarooing all the time in the mornings, and sometimes stalling. You have to be so careful when driving it. Anyhoo,
Took mine to the dealer, with a noise, basically. When I lift the clutch, i get a clunk, they say this is the gearbox and she is going in 2 weeks time to have it changed.
Have you got a clunk

??
If you have, this should be sfficient evidence that the gear chain is going. Thats what my dealer told me anyhoo.
Good Luck.