Elite: Dangerous detects my wireless Xbox 360 controller as both that and an additional joystick at the same time, how to avoid this?

More often than not when I start up the game my Custom controls bindings are gone from the menu.

I've read that if the custom controls contains bindings relying on equipment not currently present then the custom controls are not loaded, and I think I know why.

Right now I started up Elite: Dangerous and sure enough it was gone, so I took the time to set it up, yet again.

When I pick a setting and press a button on my controller it gets shown like this:

That symbol is me pressing the left cross-button below the left analog stick.

However, after some time in the game I realized I had forgotten one binding so I went back in there and now things become incorrect. I went back to the exact same binding shown above to get a concrete example and rebound it, showing this:

So it seems that after some indeterminate time my single Xbox 360 controller registers as a Xbox 360 controller as well as a separate joystick, so that for the game it looks like I'm pressing buttons on two controllers at the same time and this is recorded as my binding.

I assume that the next time I restart my computer and load up the game it will read the single controller as only a Xbox 360 controller, and thinking that extra joystick is gone, refuses to load my custom setup.

Is this a known problem? Is there any way to fix it? Is this a PC problem perhaps and not a game problem?

This is Windows 8.1 and stock Microsoft drivers for the Xbox 360 controller.

The control panel only shows my Xbox 360 controller, which is correct, I do not have any other game controller device hooked up to my computer, nor have I ever had it (this computer is 3 days old reinstall-wise, no PS4 controller or anything ever been connected to it):