I have an '07 RX350 that had a rattle coming from the back, sounded like the roof rack, or maybe from under the car. I found it to be the two little tabs near the hatch opening that lock the cover in place when it's pulled to the back. I pushed these two tabs down and forward, without the cover in place and the rattle is gone--Great! no trip to the dealer.

Not to rain on your parade but this is a well known problem with the RX. A search of this site will turn up the same solution. When I bought my RX the dealership advised me of the rattling clips (tabs) and how to avoid the rattle.

This problem can be solved permanently - my dealer replaced the 07 trunk lid tabs and the rails that the cover sits in with the 09 parts. The 09 parts no longer have the little glue on stickers on the ends of the trunk tabs that always fell off on mine. All 4 pieces need to be replaced. Now I can use the cover with the auto re-track working and not rattling.

If your car is still under warranty - go back to the dealer and have them fix it right.