Mine wasn't the amp rack. I had taken out the amp rack and it's sitting in my closet. Mine was from too much bass. It was causing the rear deck lid to vibrate against the metal it is clipped into.
I went to Home Depot and bought a package of 1/4" weather stripping for like $5. I took off my rear deck lid by pushing up all the clips from the underside (inside the trunk). You may need to unbolt your amp rack to access these clips (mine was allready out). Then I put the weather stripping around the entire underside edge of the rear deck so it would be between the plastic rear deck and the metal it attaches to. Reinstalled the rear deck by popping the clips back in place and I've now been rattle free for about 4 months.
