Have had exactly the same with mine. I had everything out to try and find it. Out went all the trays/contents in the two storage compartments in the floor, the spare wheel jack and tools, the warning triangle and the panel cover its behind, all the rear seats and squabs including the load cover and yet still there was the rattle. Further investigation revealed that the carpeted panel on the tailgate was loose. It seems that in prior ownership this had been removed and not refitted properly. My indie advised there are lots of locating lugs and clips besides the plastic 'rivets' holding the bottom plastic panel and sides in place - a 2 man job to ensure everything locates correctly on re-assembly.
So panel refitted properly and.......still a rattle. Everything had been put back after the original investigation process, but the conclusion I eventually reached was that whilst that tailgate panel had been loose, the load cover was also rattling. Odd thing is that when its out of the car and I shake it, I can't get it to rattle - I think that when its retracted the flap that hangs out is whats moving when I'm going over bumps, as the rattle is much reduced when its extended. Next time I get to her I will try removing the load cover box which (I hope and pray) will confirm this diagnosis, 'cos an E class should not rattle!
So my money is on it being your load cover box. Good luck - let us know how you get on.
