I had the same
problem and have now fixed it.
I had two types of rattle - The first a one which only shook over larger bumps and the second a near constant one.
The first was easy... there is a loose metal loop at the rear of the boot (nearest looking in). i foound out that this was shaking over large bumps. I then relised what the velcro strap was for which someone had stuck to the side of the boot carpet.....It locks the metal loop in place. No more rattle here. This loop and strap are for fitting a warning triangle box.
The second more difficult. It was coming from the boot panel. Mine was not secured correctly. Just the sort of cutting corners, amature, heavy handed workmanship you can expect. from a main dealer!!!
I would not bother taking it off unless you are sure its a
problem..... Either its not secure in places or when you knock it with your hand you can hear the rattle. If the metal clips that secure the panel are not fitted correcly (like mine) then these will rattle like hell.
Here is a quick
guide to removing the panel.....
Its in 2 parts. So you may only have to remove the main part if you are lucky.
MAIN PART.
.....First remove the 2 screws located in the inset handles. Now the panel is held by the metal clips. There should be at least 6 although mine only had 3. The technique is to find where the panel is clipped and apply force in that area only. This will ensure the panel is not damaged (like mine had been). Once you get the first couple near the screws the others will follow easy. The tricky bit now is to make sure the correct direction force is applied to the two joint areas where the main panel meets the secondary panel. BE CAREFUL.
Now with the panel removed, inspect the inner face. you will soon see how the clips work and notice if there are any missing (order from SEAT) and if any were incorrectly fitted (these will be left in the metal panel of the boot and will be rattling constantly).
Once the clips are installed in the plastic side its dead easy to clip the panel back on, making sure you hear the pop of each clip being correcly located.
SECONDARY PART
...My panel was so badly fitted I had to remove this as well to get to the rattling clips.
Take off the main panel as above. the secondary panel is held on by clips only 6 in all. Use the technique to locate each clip in turn and apply the force directly to it only NEVER PEEL FROM ONE PLACE.
Not too difficult. Now inspect the panel for missing clips and inncorrect fitting clips.
refit in the same way as the main panel. refit main panel.
The whole panel should now be firmily clipped to the boot and no annoying rattle noise
There is a constant rattle over bumps coming from the bot somewhere, first i thought it was the exhaust but i have given it a good tug around and doesnt seem to rattle. Just wondered if anyone had experienced this before and what you did to solve it? 
