I've recently run into the problem on the game Party Project, and I think I might know what the problem may be. It seems like SDL is failing to initialize, and that's what's causing the problems with the controls.
SDL seems to standardize to DInput (PlayStation/Nintendo) controllers, rather than XInput (Xbox) controllers. The DPad is a POV axis (I think) on XInput controllers, while it's regular buttons on a DInput controller (12, 13, 14, 15). And the Start button, which SDL has as button 9 in its API, seems to be L3/Left Stick Click on an XInput controller, which explains the odd mapping.