I found the problem. I modified the session options to allow the root user to 
start a session.
I started a session as root, then opened firefox, changed the settings and 
closed it. In that moment for a strange reason it saves the settings to HOME/yo 
( yo is my default non-root user ) instead of in /root
See this other screenshot, the 
HOME/yo/.mozilla/firefox/vkuuxfit.default/prefs.js attributes are reset to 
root-only... so when "yo" changes the settings they cannot be saved.

** Attachment added: "root.png"
   http://launchpadlibrarian.net/19163261/root.png

-- 
Ubuntu 8.10 : Firefox does not save user settings well
https://bugs.launchpad.net/bugs/291933
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