Spoke to me dealer today and he too suggested it might be Min's balls knocking around!

Gave me a simple test to find out if it is: take out the parcel shelf and perform usual routine, if you can still hear thudding then it aint the shelf. Simple ey!
I did this and could still hear thudding, so Min's going in next week for a check. That and the whistling noise coming from the windscreen area, oh and the other general rattles and knocks!
Not bad for an 11 day old Mini!
