Have you checked to see if this is because of a permissions problem? It sounds like what it could be. Go to your home directory and make sure everything in your hidden ".gconf" directory is owned by you (not root). Also check the files and folders within that directory too.
The graphical way:
You can see the permissions by right clicking on any file or folder and select properties then go to the permissions tab.
However, to change the ownership permissions of those files you will have to run your file browser as root.
then browse to 'filesystem' on the left, then /home/yourusername
You can change the permissions by right clicking on any file or folder and select properties then go to the permissions tab. Remember that if you are changing permissions to an entire directory, that you need to select "apply permissions to enclosed files".
The command way:
To check all files and folders in that directory, paste this command in the terminal:
Use the enter button to see more results.
ls -alR ~/.gconf | more
If anything aren't owned by you then you can use the chown command to gain ownership of the files and directories:
sudo chown -R yourusername:yourusername ~/.gconf