Woshua: Hmm. A situation such as you described can occur with an HOTAS sytem that has seperate parts, that are recognized seperately by windows. However, it's, as you say, a sidewinder (That's a legendary stick by the way).
Do you have other gaming devices attached?
What is showing up in the "Set up USB game controllers" panel in the configuration screen of Windows?
(Also, does it prevent you from playing hte game proper? Sometimes it's just better to wing it and don't delve deeper in this strange world).
I also have a gamepad. The joystick shows as "Microsoft Precision Pro USB" in Windows, and I have it set as the primary game controller. And I can still play the game, but I recently had to do some maintenance on the joystick and when I plugged it back in, the game was recognizing the joystick inputs as different devices. Instead of the POV hat being ID5, it's now ID13. I had to rebind everything again. So I think it's an issue that needs a solution and an explanation as to why the joystick inputs are being recognized as ID1, ID2, ID3, ID4, ID5, ID13, when the game's default bindings are all for Joystick 0.