Yeah I had the same thing with my FR! Never got to the bottom of why it happened despite taking everything out of the boot - including the spare wheel and raised boot flooring (the polystryene foam stuff). Came to the conclusion that it must have either been the rear seat hinges or the seat folding locks, or from inside the tailgate itself.....
In the end of the day I didn't think the noise was worth complaining about as the local dealer had problems dealing with obvious warranty issues, let alone a small rattle from the boot area....
wahooooooo! I hate rattles! I can live with them for like two minutes! then I'm like "RIGHT THE CAR MUST COME APPART! I NEED TO GET RID OF THIS RATTLE!!!!!"