I experienced this too after uninstalling xserver-xgl and restarting X. However, I think the dialog could be more user-friendly. As it stands, there's no way of telling which of the system keyboard settings mentioned in the dialog is the "X settings" and which is the "GNOME settings"; it's fifty-fifty you'll get it right if you're an inexperienced user.
I experienced this too after uninstalling xserver-xgl and restarting X. However, I think the dialog could be more user-friendly. As it stands, there's no way of telling which of the system keyboard settings mentioned in the dialog is the "X settings" and which is the "GNOME settings"; it's fifty-fifty you'll get it right if you're an inexperienced user.
Or am I missing something?