Thoughts and suggestions:

First make sure the Sonnet and the video card are firmly seated in their slots.

Tape/glue some plastic onto the inside of the lid, above the Sonnet and video cards, so nothing can touch the metal sheet lining. Make it fairly strong plastic (ie, not sandwich wrap) so things can't poke through it.

Does your video card have the external thumb screws in place, that hold it steady from the rear? Does it have the metal/plastic angle bracket that screws onto and covers the video card?