Yes it turns out that the custom Retropie xpad driver was the culprit. I was pointed to this issue thread here, https://github.com/RetroPie/RetroPie-Setup/issues/3379
I tried uninstalling and once again my XBox One controller worked fine with the program im working on (Chiaki)!
I'm still waiting to hear if that solves my user's similar issue as well.
Thanks!cgutman created this issue in RetroPie/RetroPie-Setup open xpad triggers_to_buttons=1 patch breaks SDL gamepad mappings #3379