I believe the relevant file with the settings from the keyboard
preferences control panel is:

$HOME/.gconf/desktop/gnome/peripherals/keyboard/kbd/%gconf.xml

Here's what it looks like on my freshly installed 8.04.01 system (where
the caps lock -> control setting in the control panel is not effective
after a restart):

<?xml version="1.0"?>
<gconf>
        <entry name="options" mtime="1228022444" type="list" ltype="string">
                <li type="string">
                        <stringvalue>ctrl       ctrl:nocaps</stringvalue>
                </li>
                <li type="string">
                        <stringvalue>Compose key        
compose:rwin</stringvalue>
                </li>
                <li type="string">
                        <stringvalue>eurosign   eurosign:5</stringvalue>
                </li>
        </entry>
</gconf>

Note the first <stringvalue> in the <entry name="options"> section.  It
looks OK to me (it's the same info as what the above workaround said I
should put in /etc/X11/xorg.conf), so I'm not sure why it wouldn't be
working.

-- 
caps lock as additional control broken on intrepid
https://bugs.launchpad.net/bugs/287714
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