You can delete this post. I now have it working. I think the onboard bluetooth just takes longer than my USB bluetooth dongle to become available. With the USB dongle, I could start the controller when I first saw the retropie screen, and it would sync up. Now I have to wait till until it is completely booted, then turn on the controller.
Hi, how did you achieve it?
I have the same problem, Rpi3 with the berryboot 3.6 image and I couldn’t make the bluetooth and WiFi working. I followed your same steps and no luck.
If a use the my bluetooth dongle the controller (at least) pairs but every time I turn on the Pi it didn’t reconnect, I have to go to the bluetooth setting and pair it again…
Unfortunately, no idea what might be wrong. I did everything I posted in the first post, and mine works. I just have to wait till EmulationStation is 100% booted before I turn on my controller.