I have a trunk leak issue....specifically once it rains or after washing the car a large amount of water gets trapped between the layers of the truck deck. It is noticable two ways...first, you can hear it "shoshing" when it opens and closes. Secondly, the water tends to find its way out around the latch as well as the seams. The seams being along the edge where the two layers are attached. Where and how does this water enter the cavity of the trunk deck? I have a concern for rust developing over time.
Trunk Deck Leak on 2006 Mercedes-Benz E320 CDI
There has to be either a defect in the trunk lid where it is suppose to be seam sealed (more than likely the case) or you emblem is not sealed all the way and water is getting in through the holes where these fasten. If you are still in warranty, I'd see if the dealer would take care of it. If you're not then head to a body shop