It appears that gnome get its keyboard settings primarily from X (!)
/etc/X11/xorg.conf:
Section "InputDevice"
Identifier "Generic Keyboard"
Driver "kbd"
Option "XkbRules" "xorg"
Option "XkbModel" "pc104"
Option "XkbLayout" "dvorak"
EndSection
If you put the correct settings in xorg.conf, gnome is not misbehaving
anymore.
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Gnome Keyboard layout changes are lost after reboot/-start
https://bugs.launchpad.net/bugs/23762
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