I am not all that familiar with the Mark V:25 so I had to read the manual first. I see it is a dedicated FX loop so when ever a cable is inserted into the send and return jacks, the internal connection is broken and signal must coupled through a bypass cable or through an effects device.
You either have one of four issues.
- The cable you plugged into the send or return is not making good contact to the tip of the plug inside the jack on the amp, or at the FX unit. Something could be inside the jack preventing good connections. Things like spiders find those small 1/4 jacks to be nice homes if they were left open for a while. If you have cables plugged into the jacks, that is not the case then. More than often, it is not having the cables pushed all the way into the jacks of the FX loop or the FX device.
- The send/return is connected backwards on the fx unit.
- bad cable, internal short. I have seen some poorly made cables in my day, wire not stripped properly and has frayed or loose wires. Depending on the amount of stress placed on the cable, any bending can translate into movement of the frayed wires to make contact to the shield. Also ended on rolling a 412 cab over a plug end once, that damage the plug and it was a permanent short.
- bad cable, open circuit/broken wire. That I have come across as well. Bad solder joint or broken wire.
You stated the cables were used as loopbacks, I assume you mean you tested them in the FX send/return jacks to confirm they work?