You might have hit the GTK+/GNOME feature of redefining menu accelerators by typing the new shortcut while hovering over the menu item that you want to change the shortcut for.
What is the output of these? gconftool --get /desktop/gnome/interface/can_change_accels grep -v ';' ~/.gnome2/accels/epiphany-browser -- bye, pabs http://wiki.debian.org/PaulWise
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