It started happening to me just now. Have been busy with it for hours now. My controller (Nintendo Pro) won't even connect normally anymore (green and blue light on). Have disconnected and reconnected countless times. Even switched off my mouse and disconnected my keyboard, restarted my computer, but nothing is working. I've tried every possible setting in Steam, because a lot of websites/forums tell to disable Steam Input, but then nothing works or even connects. This is absolutely beyond frustrating. Glad I got to play my first playthrough without all this happening but this makes me quite mad when it is constantly happening. I've stopped playing my current playthrough until it is fixed.
Update: ofcourse I couldn't let it rest and found a workaround/sort of fix? But only for the Nintendo Pro controller.
I simply don't connect the controller until I'm in the starting menu of the game. After intro/start-up scene and 'click random button' screen, you get the menu screen. At that point I connect, tried several times to be sure and it works. Both lights on the controller are on (blue circle and green square (bottom side)) and all is fully functional, no random (and very annoying) keyboard keybinds in the interface.
Update 2: well.. it was fun while it lasted. I'm back where I started. Keyboard binds keep popping up.