I see what you are asking... I think this is the same issue I´m having:
https://github.com/Aloshi/EmulationStation/issues/468
So... I only have one USB port used at he moment:
https://imgur.com/a/bHokk
This is connected:
https://imgur.com/a/pxkR5
That´s it, but ES sees controllers from #0 to #5:
https://imgur.com/a/Ub9j8 - https://imgur.com/a/6xcLM
Detecting 6 game-pads
https://imgur.com/a/679UD