I seem to be having the same problem. I have run the rpi-update and updated the system via apt. Any specifics on how you fixed it?
EDIT: After using the Setup PS3 controller option in the Retro setup script I updated the firmware. After a reboot the controller now only shows the 1 led. Its nice that it is not blinking all of them anymore but the default profile is still ignored. For example if I edit the profile to disable LEDs all together it still lights up the 1.
Also trying to stop sixad in a variety of ways doesn’t disconnect the controller. I try just running ‘sixad –stop’ or ‘sudo sixad –stop’ and even ‘sudo service sixad stop’. It seems to have no effect on the connection status of the controller :/.
Also I cannot get more than one controller paired at a time. Both have their macs set via sixpair but only one will connect at a time. The other just blinks until it times out. This is considerably harder than expected :/. Using version 2.3.
