With respect to multiple power supplies in the system, the Grounds should all be tied together inherently, as the load modules Gnd pin is connected back to the main board.
Now, that said, I have seen a case in the past, where we were using control transformers to provide 12v ac to chain two motors together, so if one started the second started. I don't remember the exact setup, but I did see where voltage would come out of a wire on one transformer, and complete the circuit by being connected to a wire from the second transformer 30' away in a completely different enclosure / power source. A better way to picture this,, is cut all but one pin off of two power supplies, plug them into the wall,, and have them work by connecting both to the same circuit. Converting to DC normally avoids this issue,, but depending on the quality of the power supply, just a thought.
This would be similar to having two car batteries, connecting only the positive terminal of one of them, to the negative terminal of the second one, and having them melt down because they were short circuiting.
The other scenario that I've had,,, for example when debugging,, watching buttons being pressed that are NOT being pressed,,, is reboot the computer. I've just gotten to the point where when I'm deploying on site software,,, I reboot as I arrive on site. I've seen this happen about 5 times over the last couple of years,, where I spend a couple hours trying to figure out what I was doing wrong,, to have the solution be a restart.