@SirBeethoven, apparently this is a n3DS only problem, I've make some tweaks although I'm not exactly sure that it will help, can you check again with these builds ?
http://buildbot.libretro.com/.aliaspider/2016-04-18_RetroArch_3dsx.7z
http://buildbot.libretro.com/.aliaspider/2016-04-18_RetroArch_cia.7z
http://buildbot.libretro.com/.aliaspider/2016-04-18_RetroArch_3dsx.7z
http://buildbot.libretro.com/.aliaspider/2016-04-18_RetroArch_cia.7z