Ok, here's another for you to try - this is for the gen1 models:

Normalization

• 1. Press and hold slide/tilt sunroof switch in the ”Lift” direction.
  2. In the event of delayed starting or sudden stopping of the slide/tilt sunroof, continue pressing the switch in the ”Lift” direction.
  3. After reaching lift end position, keep switch pressed for approx. 20 seconds further.
  4. Normalization is only completed when the slide/tilt sunroof closes.
  5. Release switch.
  
  The characteristic curve is learnt manually in the following stages following normalization
• 
  1. Release slide/tilt sunroof switch after normalization for max. 5 seconds.
  2. Then hold down the switch in the raising position direction until such time that the slide/tilt sunroof has returned to the closed position after a complete opening movement.
  3. This concludes learning of the curve. The switch can now be released.
  

Cheers for trying to help.

Thanks for trying, it was worth a shot...

Hi,
 Just tried:
1) With the roof fully closed. Pushed the button forward to the closing position & held it for 80 seconds. Both parts of the roof opened to the first position and nothing else.
2) With the roof fully closed. Pulled the button rearward & held it for 80 seconds. It fully opened and stayed open.

Closing the roof was the same as it has been with repeated short movements.

Here is a reset procedure for the 2nd gen models, but it might be worth a try:

1. turn ignition on and press the sunroof operating switch into the 'closed' position and hold it there. 

2. the sunroof will move a few centimetres - continue to hold the switch in the 'closed' position for approximately 75 seconds. During this time the roof will open completely, then close completely. now release the switch

Some have reported to hold the switch to the first position instead of all the way before it worked - try this if the first doesn't work.

Yes I have tried this & it made no difference.
A slight correction refresh on what I said before but not much different: When I start the opening process by holding the button, it will in-fact open both, close 1 & continue to open completely (as per normal I guess). but hold the button in the close direction it then only moves about 4 inches so I have to repeatedly press to close it. When it reaches the final closing point, it over-runs & re-opens to the first stage again so I then have to press once more making sure to let go quickly so it stops at the closed point.

Does the sunroof glass behave any different if you helped the glass by hand as it is opening? I would think this would change the behavior if resistance in the tracks is causing your sunroof to perform incorrectly....

That would make sense but I am reasonably sure that it was all quite free before I installed it. Any hints on how to check this without removing it?

Sounds like the track is binding, and the motor shuts off sensing a high load, like when a small child's hand is caught in the works.

As usual, there are those who have something to say & those who just have to say something.

well. guess you should have bought a Classic mini.. No problems. here.. bc

Hi,
I have replaced the sunroof on my 2006 2nd gen Cooper S. Now when I go to use it, it only moves in small stages. press the button & it will open front press again & it will open second window. again & rear closes / front moves back a bit / again & it moves back further. a few stages to fully open. the same closing again but when the final close step is pressed, it closes then opens again so I then have to reverse it in order to get it closed.
I guess it needs synching to something.
Any useful help please?