Ok, so now you can successfully configure the pad for Emulation Station and navigate the menus but it fails after reboot, correct? You are not having problems with over-responsive buttons anymore?
I have no idea why the pad is not responding after reboot, could be power issues. Try unplugging any other usb devices.

Can you confirm the pad functions correctly with jtest:
jstest /dev/input/js0

Regarding the input config menu (configures controls for the Retroarch emulators), the script does not work, to manually configure controls see here:

Input configuration script fails, bindings are off