the configuration dialog you use is made to work under GNOME, it doesn't apply settings but just writte configurations than gnome-settings-daemon apply, under a GNOME environement that's transparent to the user. Now for some reason gnome-settings-daemon is not running for you, option would be to display a "that configuration can't work out of GNOME" or to run the settings daemon which it's doing now
the configuration dialog you use is made to work under GNOME, it doesn't apply settings but just writte configurations than gnome-settings- daemon apply, under a GNOME environement that's transparent to the user. Now for some reason gnome-settings- daemon is not running for you, option would be to display a "that configuration can't work out of GNOME" or to run the settings daemon which it's doing now