I just disabled ALL shortcuts in Options -> Controls, and now Fn combos and my volume control do some really weird stuff. During a battle, it ended the current turn, opened the options menu, prompted me to abort the mission, and also brought up the firing modes menu for the selected soldier's weapon - and all of this happened at the same time.
It appears that this bug triggers when a shortcut is unset. In my preferred configuration, I did disable the night vision shortcuts (never needed it before, so I disabled it to avoid messing with it accidentally) - that's why it turns on with my config file but not with the default one. "Select Previous Unit" is unbound by default, and I haven''t touched it. If I bind it to anything, it no longer activates when I use the Fn key or the volume control.
In OpenXcom, "Select Previous Unit" is bound by default, that's why the bug doesn't happen there. But if I unbind it, it starts triggering to. So this is actually an issue from upstream, it seems.