I learned the lesson too.
I did a clean reinstall of raspbian jessi and started from 0. Now I had no issues installing or starting emulation station.
But I have a problem with my gamepad, that I can´t fix after several hours reading, reinstalling all again , etc.
I can read "1 gamepad detected" on emulation station, but when I press a button for configure, nothing happens.
lsubs command show me my logitech rummblepas 2 is detected too. I don´t know what more to do.
Even tried with a wired PS3 gamepad, and is the same, it is detected, but nothing happens when a button is pressed.