Every single time I'd connect to my system remotely via VNC, the next time I'd login on the real console X session, I'd get this annoying popup which says: The X system keyboard settings differ from your current GNOME keyboard settings. I've finally managed to defeat this popup (1 down, 47,321,257 more to go :-). I put this in my ~/.xsession file before it starts gnome-settings-daemon: /usr/bin/gconftool-2 --recursive-unset \ /desktop/gnome/peripherals/keyboard/kbd.sysbackup I still have no idea why running VNC causes this key to spring into existence, or why the settings don't always default to the X settings (since the documentation for the other keys near this one implies that always using X is what the system will do). If I could begin to imagine if this is even a bug and further imagine if it is a bug in vncserver or gnome or X, I suppose I'd submit a bugzilla, but since I have finally squashed it, I'm content with my solution - I won't strain my brain any more trying to decide what category the bug should get :-).