Good point on the license frame...I've heard some of them rattle like crazy on loaners. It sounds more like a buzz though.

This is a distinct thunk which the dealer has fixed once already by adjusting the rubber stops outwards. The rubber stops are now deformed w/ indentations from the hatch, so that's probably one reason it occasionally thunks (and the left stop wiggles like it's about to fall out)-:

Your problem is relatively easy to fix. I clipped someone's notes on fixing it:
http://www.keysolutions.com/M-Class.nsf/aac7d56ca8fd884b852563be00610639/9ccce0546c7ef00b85256e4a007aec4d