I've had my FR-S for a few months now and that chronic rattle apparently coming from the back window/trunk area was bothering me intensely! Thought I would share a way to finally fix it:

Open the trunk. Look inside on the left (drivers side for LHD. Just to the right of the trunk light on the underside of the rear deck you will see a bolt. A couple of inches toward the rear of the car from that bolt you will see a small metal tab sticking out of a small hole.

Bend that little tab slightly towards the bolt using a pair of pliers so you can pull the tab down while bending it in so that it holds down tightly the bit that is rattling.

Rattle gone! If it is still there but faint, bend the tab a little more.