I haven't had this happen, but multiple times during gigs my mfc has locked up, had to unplug and reboot it( not the Ax Fx) Talked to support, sent it in , they found no problems, couldn't reproduce it. My conclusion is when changing scenes and hitting another button at the same time it will freeze sometimes. Very easy to do since they are so close together.
This is my general experience with computers. For me the #1 thing that's typically gone wrong is related to quickly or repeatedly doing something that the poor software would have trouble managing (in MS windows case the other issue is memory leaks and issues requiring regular rebooting - not sure if Fractal has ever had this issue - I have not seen it).
The logic of the multi-tasking software, with each piece involving a driver component, in firmware or software or both, to me seems depending on prediction and following of timing and sequences. IOW by its nature it must respond to large lists of possible sequences. Having the latest updates helps, as does keeping each item freshly booted since presumably there may be some sort of accumulation of an unpredicted condition.
For example I have many usb drives connected connected to hubs. I have learned that one of the drive lights goes out, and that this is somehow related to the other drive on the same usb 3.0 hub not being seen. Google searches have been futile, and no new driver is available. My solution, although it doesn't make sense, is to turn on the usb drive manually about midway into the boot of the pc (even though the little button is not ever tuned it off manually for any practical reason). As soon as I began doing this I stopped having the problem. At first I didn't realize that the drive I am restarting was not the drive failing to connect. They are both on the same connection, but one affects the other somehow, and presumably the usb signal is two way and must comprehend the two drives one way or another. - so one being "unreachable" rather than in a definite state would be a monkey wrench. This is just years of experience with monitors and devices having issues that purportedly would be driver related.
At least with the Axe FX and MFC you are likely to get updated and no longer have an issue as long as a couple of people can isolate when it happens.
The key question to me would be, as implied by RDH, does the OP's issue happen after switching from a scene and also, nearly simultaneously switching another MIDI CC or more likely controlling something with a MIDI pedal? And this might leave one of the parameters of one of the new scene's blocks in an unknown state with respect to something related to the Global functions. Buggers! Just thought I would speculate because I'm always having these kinds of problems hooking things up. I have, like 12 usb devices or more running at all times as well as several MIDI devices; I'm always the first to cause a glitch in the PC world. Fortunately since the II, Fractal hasn't every caused anything; its been reliable and I respect the programming immensely.