I wondered if you're getting issues from having the boards sitting on that pink bubblewrap. It's antistatic, hence may have some level of conductivity - maybe even enhanced by humidity - so it could feasibly be affecting the connections on the underside of the PCBs. Since you seem to be getting noise related issues, I'd suggest replacing that with something a bit more inert. In an ideal world you'd screw the PCBs down with spacers off a backboard of some kind, so nothing touches the backs of the PCBs. But for starters you could always try a bit of hardboard or MDF in place of the bubblewrap? Easy to try even if it's not the cause of the problem!