Problem with 2nd Controller mapping

So I’m using xinput via the SCP Toolkit with Retroarch. When I load games with snes9x the first controller always works, no problem. The Second controller, which is setup correctly in the settings (I’ve checked, believe me) only works if I remap the controlls every time I want to use it. If I exit retroarch / start a new game with emulationstation, the controller still shows up as connected and the buttons are still correctly mapped under input but the controller isn’t found by the game, as if it wasn’t plugged in. If I remap it, it works.

I believe this isn’t an SCP problem, as the controllers both work without issue with the dolphin Emulator. Does anybody know what might be causing this problem? Help would be greatly appreciated, as I’m about to go crazy.

I’m running Windows 10 x64, Retroarch 1.3.4 and SCP Toolkit 1.6.238.16010 (Latest).