When my mini (2009 with less than 2,000 miles) is cold I notice (both hear and feel) a clicking or clanking noise under the car. I think its coming from when my auto transmission as it shifts from first to second gear.

Once the car is warm ... whether I continue driving and down shift or turn the car off and start up again it makes no difference the sound goes away.

I'm wondering if anyone else has this problem and if in fact it is the transmission or something else...

 

I had a similar problem. Dealer found out the noise was caused by transmission mount. BTW mine is auto tran.