Kerbal Space Program

KSP Version: 1.0.4 Fresh STEAM install on Win7 x64, also on Win10 x64
Mods/Add-ons: Reproduced on both a clean install and with a variety of add-ons and mods.

What happens: When first installed, everything is normal. I change my video and audio settings to my preferred default and apply/accept the changes. At this point, all settings are correctly being saved in settings.cfg (see settings.cfg.original). After I plug in a USB XBOX-360 Afterglow controller and proceed to configure the axes, I decide that I don't like that as a control method and decide to stop using it. Now, every time I start up KSP (without the gamepad plugged in) the audio and video settings are reset to the default settings no matter what I configured previously, but the axis configurations remain what they were after configuring the gamepad (as shown in settings.cfg.bad).

Fixes/Workarounds: I found the following section in settings.cfg and replaced it with the code from settings.cfg.original, then started the game, and everything appears to be working normally.
settings.cfg:

AXIS_PITCH
{
    PRIMARY
    {
        name = Controller (Afterglow Ga.
        axis = 1
        inv = False
        sensitivity = 1
        deadzone = 0.2422314
        scale = 1
        group = 0
        modeMask = 7
    }

AXIS_PITCH
{
    PRIMARY
    {
        name = None
        axis = -1
        inv = False
        sensitivity = 1
        deadzone = 0.05
        scale = 1
        group = 0
        modeMask = -1
    }