I started getting these errors recently from a number of systems, as well as failures in operation. The cause appears to be scripts/programs running as root trying to contact the user gconf daemon. This is "stupid" so how can I work around it. One case I am trying to fix is hibernate scripts resetting the background on a laptop before it shuts down - fails. Another is killing evolution from root when it dies, wont exit etc.
Billk GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://www.gnome.org/projects/gconf/ for information. (Details - 1: Failed to get connection to session: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.)

