"Controller not configured" Error Message

[darkblaster77]

Pi Model: 2 B
RetroPie Version Used: 4.1
Built From: Pre made SD Image on RetroPie website
USB Devices connected: Nil
Controller used: Sony PS3 Wireless Controllers
Error messages received: Yellow wordings "controller (xx:xx:xx:xx:xx:xx) not configured" at start of games
Log found in /dev/shm/runcommand.log (if relevant): Nil
Guide used: https://github.com/retropie/retropie-setup/wiki/Setting-up-a-PS3-controller
Emulator: lr-fbalpha

Problem Encountered
I am trying to have a single config file for multiple PS3 Wireless Controllers, as I am using the same image for my brother's set.
Followed the steps under Manually setting input, from the guide stated above.
Whenever a game is started, it would display "controller (xx:xx:xx:xx:xx:xx) not configured".
And I would not be able to use the PS3 controller in the game.
Have to exit the game with a keyboard.

Additional Info

1. Both controllers are working fine in ES
2. These steps are working for RetroPie v.3.8.1

Manual setup in retroarch.cfg would work, but this will limit to one type of controller.
Have a couple of Hori Fight stick as well.

Please advise.
Thank you.