I think I found at least a log showing my problem. ES_LOG event after exiting the retroarch gui. Not sure what this looked like when it was actually working on the system. I'll work up the temp button for now..
Jul 21 03:20:56 lvl2: Added unconfigured joystick Ultimarc UltraStik Ultimarc Ultra-Stik Player 4 (GUID: 0300000009d200001405000011010000, instance ID: 20, device index: 0).
Jul 21 03:20:56 lvl2: Added unconfigured joystick Ultimarc UltraStik Ultimarc Ultra-Stik Player 1 (GUID: 0300000009d200001105000011010000, instance ID: 21, device index: 1).
Jul 21 03:20:56 lvl2: Added known joystick Sony Interactive Entertainment Wireless Controller (instance ID: 22, device index: 2)
Jul 21 03:20:56 lvl2: Added unconfigured joystick Ultimarc UltraStik Ultimarc Ultra-Stik Player 3 (GUID: 0300000009d200001305000011010000, instance ID: 23, device index: 3).
Jul 21 03:20:56 lvl2: Added unconfigured joystick Ultimarc UltraStik Ultimarc Ultra-Stik Player 2 (GUID: 0300000009d200001205000011010000, instance ID: 24, device index: 4).