I have noticed that when pairing my bluetooth controller (GameSir G3s YES I KNOW IT HAS ISSUES IN THE COMPATIBILITY LIST) that it works flawlessly in emulation station. Once the emulators launch, however, there is no functionality at all. While testing some of these options I realized the only time I see the retroarch message "100% connected [insert controller here]" is when I send an SSH reboot or poweroff command.
I stopped emulation station as well to see if it was holding onto the bluetooth handshake, but never saw that message.
Looks like something is not pushing the bluetooth controls over to the launcher.