Comment 7 for bug 209493

This bug doesn't seem to be present in 8.10. Thanks for chasing it up!

The error was still appearing after the upgrade, but I bumped the settings in Keyboard Preferences, which I guess caused the config to be re-written. The outputs of the above commands are now:

$ xprop -root | grep XKB
_XKB_RULES_NAMES_BACKUP(STRING) = "evdev", "jp106", "jp,jp", "106,", "grp:shifts_toggle,lv3:ralt_switch,grp_led:scroll"
_XKB_RULES_NAMES(STRING) = "evdev", "jp106", "jp,us,jp", ",,kana", "grp:shifts_toggle,lv3:ralt_switch,grp_led:scroll"

$ gconftool-2 -R /desktop/gnome/peripherals/keyboard/kbd
 layouts = [jp,us,jp kana]
 model = jp106
 options = []