I had a similar noise when I picked up my car. It took 2 trips back to the dealer. The first time they did not get it correct because I drove about 20 miles before I went over something that would make the noise. The second time they had the car for 2 days chasing the noise admitting that they could hear it too. If I remember correctly they told me it was an vertical adjustment on one of the pedestals that support the roof while up. I guess they raised it up to put more pressure on the roof when up and the noise went away. Now if I had only asked them to point out what they adjusted, I could be of more help.
2009 Crimson Z4 35i