Not sure if this will fix your problem, but perhaps you can manually edit the config file that contains the user keys. If you go to Documents\Amnesia\Main\<your user>\user_keys.cfg and edit it, then you can change some of the values in there.
This is what I have in mine (I haven't tested it though). It should be the default settings:
<Inventory Primary="Keyboard.Tab" Secondary="GamepadButton.Button 6" />
<Journal Primary="Keyboard.J" Secondary="GamepadButton.Button 3" />
<Forward Primary="Keyboard.W" Secondary="GamepadAxis.Axis 1.Negative" />
<Backward Primary="Keyboard.S" Secondary="GamepadAxis.Axis 1.Positive" />
<Right Primary="Keyboard.D" Secondary="GamepadAxis.Axis 0.Positive" />
<Left Primary="Keyboard.A" Secondary="GamepadAxis.Axis 0.Negative" />
<LeanRight Primary="Keyboard.E" Secondary="" />
<LeanLeft Primary="Keyboard.Q" Secondary="" />
<Attack Primary="MouseButton.RightMouse" Secondary="GamepadButton.Button 4" />
<Interact Primary="MouseButton.LeftMouse" Secondary="GamepadButton.Button 5" />
<Rotate Primary="Keyboard.R" Secondary="GamepadButton.Button 9" />
<Lantern Primary="Keyboard.F" Secondary="GamepadButton.Button 2" />
<Run Primary="Keyboard.LeftShift" Secondary="GamepadAxis.Axis 2.Positive" />
<Lean Primary="GamepadAxis.Axis 2.Negative" Secondary="" />
<Crouch Primary="Keyboard.LeftControl" Secondary="GamepadButton.Button 1" />
<Jump Primary="Keyboard.Space" Secondary="GamepadButton.Button 0" />
<QuestLog Primary="Keyboard.M" Secondary="" />
<RecentText Primary="Keyboard.N" Secondary="" />
<CrosshairToggle Primary="Keyboard.X" Secondary="" />
If that doesn't work, perhaps the entries can be modified.
If nothing of this works, I'll assume it's a bug with the game and only FG can fix it.