I've been getting this error since upgrading from intrepid alpha 4 to alpha 6.
sudo chmod 775 /etc/gconf/gconf.xml.system solved it, thanks Sebastien!

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There is a problem with the configuration server. 
(/usr/lib/libgconf2-4/gconf-sanity-check-2 exited with status 256)
https://bugs.launchpad.net/bugs/269215
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