This may sound obvious, but if you are pretty certain it isn't the guitar or amp, go through the signal path one item at a time, interconnects, boxes, etc. I will usually start with cable > amp, make sure that is working, and then introduce one box at a time until something becomes obvious as the culprit. I just have maybe four boxes on a pedalboard, so it's easy. If you have a switcher, you have a lot more troubleshooting to do, but it's all just logic and elimination. Try one item at a time (pedal, connector, switch relay) and then move on to the next until you find out what's up.