Eu tenho o mesmo problema hoje. Escrevi um pequeno script para converter as combinações de teclas antigas na nova interface.
#!/bin/bash
# Delete old new-style keybindings
gsettings set org.gnome.settings-daemon.plugins.media-keys custom-keybindings "[]"
gconftool-2 -R /desktop/gnome/keybindings | while read LINE; do
read BINDINGLINE
read ACTIONLINE
read NAMELINE
NUM="'echo "$LINE" | sed -e 's@^/desktop/gnome/keybindings/custom@@g' -e 's/:$//g''"
BINDING="'echo "$BINDINGLINE" | sed 's/^binding = //g''"
ACTION="'echo "$ACTIONLINE" | sed 's/^action = //g''"
NAME="'echo "$NAMELINE" | sed 's/^name = //g''"
gsettings set org.gnome.settings-daemon.plugins.media-keys.custom-keybinding:/org/gnome/settings-daemon/plugins/media-keys/custom-keybindings/custom$NUM/ name "'$NAME'"
gsettings set org.gnome.settings-daemon.plugins.media-keys.custom-keybinding:/org/gnome/settings-daemon/plugins/media-keys/custom-keybindings/custom$NUM/ command "'$ACTION'"
gsettings set org.gnome.settings-daemon.plugins.media-keys.custom-keybinding:/org/gnome/settings-daemon/plugins/media-keys/custom-keybindings/custom$NUM/ binding "'$BINDING'"
CURRENTLIST="'gsettings get org.gnome.settings-daemon.plugins.media-keys custom-keybindings'"
CURRENTLIST="${CURRENTLIST%]}, '/org/gnome/settings-daemon/plugins/media-keys/custom-keybindings/custom$NUM/']"
gsettings set org.gnome.settings-daemon.plugins.media-keys custom-keybindings "${CURRENTLIST/[, /[}"
done