Had similar creaking noise from behind the driver in area of top on 2010 Z4. Rattles or creaks when on rough roads with top up. Dealer (Stevens Creek BMW, Santa Clara CA) took a few days to road test and several iterations to find the issue. Something with gaskets or seals not installed properly. Good persistence on their part got it fixed, no more noise. Very satisfied! They did comment about the top being a Rube Goldberg mechanism, as I am sure it is wonderful to work on
...but maybe they found it right away and were just joy riding in my Z4?
Mike