One of the causes of the clunking noise is the top tailgate shifts when the the car body shifts. I noticed the noise even when I do not hit bumps also. The X5 body is just not rigid enough.

The good thing is that I was able to fix it and it only cost $2. the Bumpers for the top tailgate was a little worn and so I purchase rubber pads from lowes. It was used for the feet of chairs. I stuck one on each side and all clanking noises were eliminated. I have used it for several months and have not lost one yet. I keep the spares in the trunk just in case.