I’m pushing here since the mentioned thread is one year old.
Keybinding Conflict
Boarcas did described the bug perfect in a new thread: Mouse & Keyboard rebinding resetting every session
Rebind your keys, close the game and restart it, following can happen:
It shows your Custom setting, but
- it uses both, new and default binds or
- uses only default binds
Rebind your keys, play the game without closing it and it works fine for me.