I apologize, I guess my configuration information would help troubleshoot this issue.
I have searched the forum and have not found a fix specific for the xbox one controller. The basic issue seems like I can not point this emulator to use the xbox one controller configs. So if we can figure out how to get libetro 2003 to use the same controller mappings as mame4all we will be golden.
Pi Model: (B, B+, 2 B etc..): Raspberry Pi 2 -Model B - Version 1
RetroPie Version Used: 4.1
Built From: Using base 4.1 image from retropi website download link
USB Devices connected: Keyboard
Controller used: Xbox One S - Connected by USB
Error messages received: No error message. Can not back out of Emulator
File: (File with issue - with FULL path): no exactly sure what file is having issue with the configuration. My guess it is one of the files in /opt/retropie/configs/all/retroarch/autoconfig or /opt/retropie/configs/mame-libretro/
Emulator: (Name of emulator - if applicable): Mame-libretro 2003
How to replicate the problem: I was able to replicate by doing a complete reload and taking the base image 4.1 offered on the retropi website. I was still unable to configure libretro to work. When I got it to work earlier I must of done some global configuration to get it to work because I was in Mame4all and then went to libreto and it worked. Eventually something happen to muck up my controller configuration.