I have the same problem on my X5. The car has the extended cover, so I went to the dealer and they took 2 days to make a analisys. They call me yesterday saying they ordered another new complete sunroof (-glasses) to fix the problem. No cost. This make me VERY HAPPY and with a feel of reability in BMW Cover!

I'll need to wait 20 days for parts, but the sunroof was closed while we wait all stuff. I'll let you know about everything and investigate the parts involved on this problem.
Chris