Okay, after doing a completely fresh install, I’ve run into the exact same problem. However, after watching and following floob’s usb controllers parts 1 and 2, I came across a section in part 2 where goes over the system command line. I know he’s working off of 2.3 and 2.6, but the long string of commands isn’t present, so what I’m assuming is happening is the control scheme that is loading is just the same one as emulationstation. This makes sense because only the buttons that get registered by ES are the ones functioning. The unresponsive buttons are those not asked for input by ES. I’m not a programmer, though I know some bare bones basics, but it seems like the section of commands that would tell the emulator to use retroarch’s configs are missing. Any ideas on whether I’m on the right track or not?