I worked out what was causing it for me. I use an X52 Hotas Custom config but I also use an XBox 360 controller for the SRV. If the XBox controller is not plugged in, none of the keybinds work correctly. Plug it in and 'hey presto!', everything works as I expect it to.Curious as to why the “reset keybind” thing happens to some and not others.
Never had this happen. Interesting.
I never had this problem with the previous incarnations of the game btw.