I had a similar problem, where I wasn’t able to set anything in DConf no matter what tool I used (gnome-control-center, dconf-editor, gsettings, demonic forces). I didn’t try using root, though.
What I found was that I had two files in the /etc/dconf/profile directory: “user” and “gdm”. “user” looked like this:
while “gdm” looked like this:
I changed “usr” to look like “gdm,” and suddenly DConf settings worked again (and thank God, because the lack of DConf settings was preventing me from running GNOME at all under Ubuntu 12.10).
I’m not sure how well this applies to your situation, since your “/etc/dconf/profile/gdm” looks like my “etc/dconf/profile/user”, and you have no file “/etc/dconf/profile/user”. I hope this gives you some ideas, though!