Just stumbled upon this post. Perhaps making sure the SPEAKER power is OFF (and the amps have had a chance to discharge) BEFORE turning anything that feeds the speaker on/off is the correct solution, regardless of firmware/FC connection/whatev? Your speakers will thank you for it – and you won't damage the voice coils by slamming them to their physical limits.
That's good advice for the general case, but should be unneccessary with the Axe FX as they properly protect the outputs (disregarding any specific configuration issues such as the FC problem described above). It's also impractical in certain setups such as my home studio which uses a III as my PCs main audio interface - personally I'm not gonna press the power switch on the back of my studio monitors 4 times (1x on, 1x off, times two speakers) for each time I turn my PC on and off. And given how often we get firmware updates, the time for switching on/off the speakers for the new firmware restart would add up pretty fast
On the topic of user screwups with the Axe FX, I had this one happen to me on my first gig with the III:
I was still waiting for my FC-12 at the time and thus had to use the MFC-101 with the Axe III via MIDI. I had configured and tested the MIDI functionality during rehearsal. But after setting up at the venue, nothing worked anymore - pressing any button on the MFC had zero effect on the Axe. Well, not exactly zero, because any actions on the MFC would still cause the MIDI LED on the Axe FX front panel to light up, so I thought the MIDI communication was working fine and the configuration in the Axe or the MFC had gone awry, potentially due to the FW update I applied the previous day. Tried various things but couldn't find the issue in the short linecheck time and proceeded to play the gig without a footswitch. Next day back at the rehearsal room everything was working again.
To cut a long story short, the issue was that I incorrectly connected the 5-pin MIDI cable to the MFC at the gig - the MFC has a 7-pin MIDI jack and the 5-pin cable was rotated by one pin to the left. Connected like this the Axe FX didn't receive any valid MIDI commands from the MFC, but the MIDI LED still activated for some reason. The really stupid part about this is that I reconnected the cable during my troubleshooting but must have connected it incorrectly a second time...