It is hard to make suggestions not knowing how you are looking at the signal and seeing your set up.
Have you used a signal splitter at any time? I'm curious what you would get if you just split the signal with one cable going to your load and one going straight to your scope.
Knowing you only get the anomaly when your black box is connected. I would concentrate on finding the problem there. Having a different scope connection using a signal splitter would confirm the problem is the box you built or send us off in another direction.
Can you post a picture of the inside of your box? Maybe an extra shield on the pcb itself can be added with sheet copper as done in ham radio. It may just be a degree of shielding matter and your box is not sufficient for the task as is.