@jiepiewie Try using the bluetooth menu items to de-register the controller and try again. Make sure you havent lost the pairing by accidently holding the select button for 3 seconds – this wipes the pairing.
Tried and failed again. Removed the controller using the retropie-setup-menu, added it agin and rebooted the pi. No pairing whatsover. I’m stumped. On my other wheezy-installation it worked flawlessly.