I too was having the same issue with EmulationStation prompting to re-configure the controller (ps3) bindings every time on reboot, also many times the controller would not even be detected.

I finally have my PS3 controller working consistently. It turns out there was a two-year old comment on this very blog that hinted at the the solution. What’s happening is that EmulationStation is starting up too quickly — not allowing enough time for the PS3 controller to sync over bluetooth and setting itself up as a joystick.

The fix:

1. Start the retroie-setup script and disable the splash screen (there’s an option for this)

2. Edit the /etc/rc.local file with your favorite editor:

Above the “exit 0” statement enter the following:

echo "Sleeping for 30s.  Sync your controller now..."
sleep 30s

Now every time you boot the Pi, it will notify you to sync your PS3 controller (simply press the PS button on the controller), then EmulationStation will start thereafter.

On a side note, RetroPie 2.3 has a built-in controller profile for the PS3 controller — meaning you do not have to manually map buttons in RetroArch. The “hotkey” by default is the SELECT button. So SELECT+START exits, SELECT+L loads last save, etc.