There is a way to release the hydraulic pressure so you can open / close the top manually by hand. I would try this to make sure nothing is 'binding' and preventing the normal movement. 

Your owners manual has the details on how to release the top - I was able to do this on my 05 R52.

I have a 2006 mini cooper S convertible (R52) that I recently replaced the sunroof cables because a portion had broken (link). After reinstalling everything, my sunroof works great, but my top will not enter the second stage. I press the button to open the top and the sunroof opens. Then I press the button to open the top again and the locks unhook themselves and the top goes back about 2 inches but the motor never kicks on to lift the top off of the windshield pillar and the "close top" button flashes.

 

I have checked the parcel shelf and the microswitch is depressed. I have checked the reservoir, and it has fluid in it. Oddly enough, when I close the top, I can hear the motor kick on to ensure everything is seated.

 

What else can I check?