I think I ran into this problem once. I think I resolved it by literally telling it not to use sdl (–disable-sdl). I also disabled everything that I wasn’t using, just in case (all of the audio libraries expect ALSA, all of the video output except KMS, etc…)
Wow, this is pretty awesome! 
Is it possible to make RetroArch launch a command upon quitting itself? This could allow us to, say, have XBMC launch from the command line (if XBMC can do that, I think it can) automatically when you quit RetroArch, giving us a kind of Xbox 1-like experience.
Good thing you posted this. I also had to compile with --disable-sdl to get RetroArch to run in KMS mode.
You shouldn’t have to --disable-sdl. It fails because it’s trying SDL, but it’ll fail and continue to next context method (i.e. KMS). If it really errors out fully, that’s a bug.
For launching a command on exit, ever heard about shell scripts? 
I think it really errors out, because I can’t do anything after trying to run RetroArch if I don’t --disable-sdl.
I have heard about them, but I’m not skilled at using them. You create a file with both the RetroArch command and the XBMC command, but I guess this won’t be enough:
retroarch roms/md/sonic2.bin -L cores/libretro-genplus.so xbmc
EDIT: It seems that it actually is enough if you just add #!/bin/sh to the top, add the .sh extension and make it executable.
Sounds like SDL on your distro tries to use the framebuffer directly or something, and doesn’t clean up after itself … :\ I don’t have this issue here at least.
Yeah, it’s probably my distro. I removed all the SDL packages I had installed and compiled it myself, and now the issue is gone.