I had exactly this problem, going over speed humps at low speeds, when my car was only 3 or 4 months old. There were a couple of forum threads on it and a few people had the same problem. The concensus seemed to be the parcel shelf supports have balls on the end and they do knock around when the tailgate is shut.
I didn't think this was my problem though, it seemed different and part of the chassis. However, I am pleased to say that miraculously it stopped and has never returned. So I'm afraid I can't be too much help but thought I would share this with you anyway! Soz.