I have noted the various comments about this noise and have read Tom at MMMC's post.
Unfortunately I have had the same problem with my R56
MCS. Although I had the problem wither the weather was hot or cold and even when I had been out in it ,stopped briefly and then restarted the engine. (Feb 07 build)
I had taken the car to the dealership where I had purchased it .Who informed me there was nothing wrong with the vehicle. Unsatisfied with this response I took it to an alternative dealership. They retained the vehicle for 3 weeks due to trying to get the parts and refit the full cylinder head. A list of items replaced are as follows.
Cylinder Head
Inlet Camshaft
Outlet Camshaft
Roller Drag Lever (16 of)
Hdr. Valve pushrod (16 of)
Repair kit valve seal ring
set bolt cylinder head
torx bolt (part number 11367545863)
torx bolt (Part number 11367536087)
Cylinder head gasket
set of profile gaskets (part number 11127572851)
vacuum pump
gasket, oil pan
gasket W/heat prot. shield
profile gasket (4 of) (part number 11617528340)
set of sealing and fastening parts (4 of)
profile-gasket (part number 11537548658)
gasket ring (4 of) (part number 07119963151)
gasket ring (4 of) (part number 07119963201)
valve collet (22 of)
set oil-filter element
(I have added part numbers for items of the same name in case anyone thought it was a duplication this is taken from a list supplied by the dealership who fitted them.)
Followed by a 100 mile roadtest.
I haven't had the noise since but I have no faith that it is now fixed for good as I have been waiting for 8 weeks now for an actual explanation of what the problem was and why so many components had to be replaced. All I have been told so far is that I had a leaking cylinder head although the oil had been checked and the level was fine and there was no traces of oil or smell of oil.
The car now has a relatively loud tick at idle wither it is hot or cold or even when it has been used. Although I have been told that this is normal and I have heard it on others but don't remember it being as loud on my car before the problem.
This is probably the most serious of the 10 problems I have had some cosmetic ie interior panels rattling, Sunroof blinds and panels squeaking, Rubber rear window seal below spoiler coming loose, Chrome stripping on bonnet coming off, scuttle panel riding up.
Window not returning properly when door shut leave a gap when closed.
2 electrical faults - flashed up warning lights, other flashed up warning lights and said to contact dealer at not move vehicle. Both rectified on individual visits to garage by replace parts.
Some more annoying like a sunroof which doesn't open when its warm. This has had bits replaced on countless occasions over the last 13 months and has had the full sunroof replaced too and it still is not operating properly.
I've had my car since 01/03/07 and it has been in the garage for repair over 25 times. Most of which for the sunroof and the rear window seal.
I just thought I would share this because of the relevance to this post and the number of people commenting on it.
This is my third Mini and at the moment I wouldn't recommend one to anybody due to my lack of faith in the car I have.