Comment 4 for bug 989648

Further update: Apparently the keyboard settings are now scattered between gconf and dconf. The tool seems to only change the settings in gconf, while at least gnome shell uses dconf's org.gnome.desktop.wm.keybindings. (This is probably worth its own bug? Should I open another one?)

Removing the wrong Alt+Fn settings from there helped a lot. All key bindings work again sometimes, but still not continously.