not zero ohm. more likely a ferrite bead....
Ferrite beads shoot flames when they exceed their rated current, it is pretty spectacular.
Reading the thread again, I'm certain it is a isolation problem. First thing to note, this is a transient effect so you might not be able to catch it easily. You've probably already realized it.
IMO, it's not about measuring potential, you want to measure impedances.
First thing I would do (if not done already) is draw a diagram of your system with each connection.
Then identify which "ground" each block is referenced to, and where it's power is coming from (and returning!)
Then make sure that there is high impedance between "isolated" grounds. You can just use a dmm at first to diagnose gross problems which it sounds like you have. Otherwise this is also tested with a high pot or leakage test.
My thought is that you said you have a power supply and USB connection. Normally current for the system comes from the positive terminal of the ps connection and returns to the negative. That's great but USB has a ground too and if that ground is somehow connected back to the power supply negative terminal through a different system connection (or a black box like a USB hub) then there is a SECOND return path (I intentionally did not use gnd here) will share some of that return current.
Maybe that is ok normally because the ps connection is very low impedance and hence takes most of the current but if that first power supply connection has an issue (vibration, pinched cable, some other failure) then all of the return current will flow through the USB connection. If any element of that connection cannot handle that, something will smoke like said resistor or bead.
Power supplies are wired, especially the concept of "earth" or "protective" ground vs "neutral". Some supplies have a short from earth to the output negative (ones that are not labeled as "medical"). So even if you have two "isolated" supplies, they can share a ground through that "earth" connection.
I'm sorry it's terribly confusing and no simple way to explain, I've designed cardiac floating surgical devices before and we spent many months testing and certifying isolation so that's why I'm so familiar, it took me a long time to be proficient.
PM me with questions if you don't want to share diagrams with the rest of the forum, I would be glad to help.