I have almost the same problem but something different is listed twice
somewhere:

$ gnome-lirc-properties
/var/lib/python-support/python2.5/gnome_lirc_properties/__init__.py:57: 
GtkWarning: GtkSpinButton: setting an adjustment with non-zero page size is 
deprecated
  return ui.RemoteControlProperties(gtk.glade.XML(ui_filename)).run()
WARNING:root:/usr/share/lirc/remotes: Remote linux-input-layer listed twice in 
generic/devinput.conf and linux-input-layer-lircd.conf.
WARNING:root:/usr/share/lirc/remotes: Remote NEC listed twice in 
generic/NEC-pulse.conf and generic/NEC-short-pulse.conf.
WARNING:root:/usr/share/lirc/remotes: Remote NEC listed twice in 
generic/NEC.conf and generic/NEC-short-pulse.conf.
WARNING:root:/usr/share/lirc/remotes: Remote SONY listed twice in 
generic/SONY20.conf and generic/SONY12.conf.
WARNING:root:/usr/share/lirc/remotes: Remote BESTBUY listed twice in 
bestbuy/lircd.conf.bestbuy and bestbuy/lircd.conf.bestbuy2.
WARNING:root:/usr/share/lirc/remotes: Remote DVICO_MCE listed twice in 
dvico/lircd.conf.fusionHDTV and dvico/lircd.conf.fusionHDTV.
WARNING:root:/usr/share/lirc/remotes: Remote Apple_A1156 listed twice in 
apple/lircd.conf.macmini and apple/lircd.conf.macmini.
WARNING:root:/usr/share/lirc/remotes: Remote PVR2000 listed twice in 
leadtek/lircd.conf.PVR2000 and leadtek/lircd.conf.PVR2000.
WARNING:root:/usr/share/lirc/remotes: Remote Medion_X10 listed twice in 
atiusb/lircd.conf.atiusb and atiusb/lircd.conf.atiusb.
WARNING:root:/usr/share/lirc/remotes: Remote Medion_X10 listed twice in 
atiusb/lircd.conf.atiusb and atiusb/lircd.conf.atiusb.
Traceback (most recent call last):
  File "/usr/bin/gnome-lirc-properties", line 27, in <module>
    gnome_lirc_properties.run(sys.argv[1:], datadir)
  File "/var/lib/python-support/python2.5/gnome_lirc_properties/__init__.py", 
line 57, in run
    return ui.RemoteControlProperties(gtk.glade.XML(ui_filename)).run()
  File 
"/var/lib/python-support/python2.5/gnome_lirc_properties/ui/RemoteControlProperties.py",
 line 60, in __init__
    self.__restore_hardware_settings()
  File 
"/var/lib/python-support/python2.5/gnome_lirc_properties/ui/RemoteControlProperties.py",
 line 251, in __restore_hardware_settings
    settings = lirc.HardwareConfParser(config.LIRC_HARDWARE_CONF)
  File "/var/lib/python-support/python2.5/gnome_lirc_properties/lirc.py", line 
1005, in __init__
    key, value = tokens
ValueError: too many values to unpack

-- 
"too many values to unpack" error
https://bugs.launchpad.net/bugs/303910
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