I have the same problem, i write this script ->
sudo service lightdm stop
emulationstation
sudo service lightdm start
I can execute through desktop Raspbian Jessie and launch emustation and returns to x when i go out, but i can not execute anything, the script launch emulationstation but when i go to menu retropie or mame and execute a game or setup seems to be launch but anything and returns a menu of emustation, but if i execute manually the script in terminal and go to one text session to crtl+alt+f2 and launch emustation it works good and execute all the games. I thing its a problem of rrights to launch emustation in script
Please, any ideas ?? help please ;-)
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