Does this happen in emulation station as well or is it only in certain emulators such as SNES (2 player with pocketnes has issues and made it seem like my controllers were having problems but it was just a bug in the emulator)? Try testing to see if just the retroarch autoconfig files work without your custom additions to the retroarch.cfg (so change the input_autodetect_enable from false to true and comment out the joypad buttons you added) and see if that changes anything. Also be sure to only have one controller plugged in when running retroarch config (and be sure to make sure no buttons are sticking before configuration). Let me know what you come up with. I can also give you my working configs when I have access to them later if nothing else works for you.