For the box to be an effective Faraday shield, the entire peripheral of the top lid must be in electrical contact with the rest of the box. Failing this, RF can easily couple from the largely isolated plane of the lid to the internal electronics.

Also don't overlook the large opening you have on the side of the enclosure. I doubt it would allow the GPS to work but it could enable the ingress/egress of a 2.4 GHz signal.