Annoying as hell, after you edit your custom keyboard config (e.g. remapping directional movements to WASD) the game seems to loose settings and on next launch you'll have to restart with default controls.

This finally fixes this annoying behaviour.
Tested and working with keyboard remap and Steam game version 1.1.1.0, Windows 10.

(example for keyboard players)
Edit like this:
...
[WinDrv.WindowsClient]
AudioDeviceClass=XAudio2.XAudio2Device
MinAllowableResolutionX=0
MinAllowableResolutionY=0
MaxAllowableResolutionX=0
MaxAllowableResolutionY=0
MinAllowableRefreshRate=0
MaxAllowableRefreshRate=0
ParanoidDeviceLostChecking=0
AllowJoystickInput=0 (when 0 gamepad won't work)
...

Still strange things may happen if you use Bluetooth gamepad and the device turns off due to idle while playing with keyboard, and/or you switch between keyboard/gamepad controls. In this case custom control settings can be lost.

As a general rule, set:
AllowJoystickInput=1 🎮 (ONLY if you want to use the gamepad, will save custom remap)
AllowJoystickInput=0 ⌨ (if you want to play with keyboard keys, will save custom remap, gamepads won't work)
Unfortunately keeping both being able to easily switch between keyboard <-> gamepad is not possible.

If you want to play with custom settings for gamepad or keyboard without loosing them on next launch, you MUST set AllowJoystickInput accordingly.