And as he has posted the CPU board picture, I am wondering on an un-shielded SMPS mounted directly on the CPU board.
Not necessarily a problem. I have some very carefully crafted SMPSs on some of my boards without any problems. However a badly crafted SMPS can kick logic to Timbuktu even if it is well designed (design -> schematic etc, craft -> board layout etc.). Anyhow, he states that without the contactors (and in other locations where the contactors are DC) there is no problem, so I doubt it is noise from the board itself.

Erik