I just installed a fresh copy of Ubuntu 15.10 and installed RetroArch with the following commands
sudo add-apt-repository ppa:libretro/stable sudo apt-get update sudo apt-get install retroarch retroarch-assets retroarch-joypad-autoconfig libretro* sudo wget https://goo.gl/H2SViY -O /etc/udev/rules.d/99-8bitdo-bluetooth-controllers.rules ;
Yay it recognizes my controller!
However when I try to go to full screen I get the following error message in the terminal: Protocol error: bad 3 (Window); Sequence Number 5 Opcode (20, 0) = GetProperty Bad resource 1345525328 (0x50331650) at -e line 15.
If I try to start the program with “retroarch -f” the application does not start. without any error messages displayed
The screen flickers for a second, but remains in window mode. I cannot change most of the settings.
Let me know what information anyone needs to help me debug why it will not go into fullscreen. I have no problem resetting back to default settings as this is a clean install 
If it works, the nuclear approach is fine with me!
Thanks!
PS: I did install RetroArch on a VirtualBox hosted in a windows machine and I was able to go to fullscreen there.