Comment 10 for bug 516384

The second warning you get when starting gnome-settings-daemon from the terminal indicates that you're suffering from bug #389766. I'm not sure if the problems you see in Nautilus are related to this, could you verify this with a work-around for the mentioned bug?

There are two work-arounds: the first is setting the GConf key "/apps/gnome_settings_daemon/gtk-modules/pk-gtk-module" to false in 'gconf-editor', the second is to remove 'packagekit-gnome'.

Ubuntu isn't using PackageKit by default, so by removing 'packagekit-gnome' you shouldn't lose desktop functionality. However, that doesn't mean bug #389766 shouldn't get fixed.