One if the most efficient ways to radiate a signal is by placing the source in the center of a dipole antenna. If you forget the AC and DC power pathways for now and think of the SMPs as a signal transmitter, you can see both have cables leaving them at the input and output sides. Now consider that virtually every commercial and most amateur/home made transmitters are built inside screened boxes but still work efficiently, you may start to see things from the signals perspective.
Another analogy: imagine a long power cable feeding a completely screened RF source. The cable rises from the ground up a few metres to the screened box. First thoughts are the box is screened so AC goes in but nothing can get out. Now turn it upside down, the screened box is ground and the cable rises up from it. Doesn't that look like a conventional transmitter arrangement with a vertical antenna?
We really need to see a photograph of the test set up to be sure but I would be pretty sure the box is almost irrelevant in this test and the difference in RF between the input and output cables is causing the problem.
Brian.