I've been using GNOME 2.6 from Debian unstable for a month.  During the last few
days there were three occurrences where settings would suddenly stop working in
various GNOME applications.  For example, theme changes do not take effect. 
Related configuration settings stop tracking each other (e.g. in Sticky Notes
applet preferences dialog the font selection button should be disabled iff "use
system font" is selected).  It is impossible to change the visibility of sticky
notes or the background colour of gnome terminals.  Changing a preference,
closing the dialog, and going back to the same dialog shows the old state of the
preference.

It is easiest to observe the effects of this bug with sticky notes applet.  I
have selected the click behavior to show/hide all notes in the preferences
dialog.  Normally I can open gconf-editor, go to
/apps/stickynotes_applet/settings and see the 'visible' key change state wheneve
I click on the applet icon on the panel.  When this bug manifests, the key no
longer changes state when I click on the applet.

Restarting the sticky notes applet fixes the problem, but for that applet only.
 Logging out and logging back in fixes the problem for all applications.

The gconfd-2 process is running.  Restarting it does not fix the state of
affairs.  I have observed with strace that gconfd-2 does some communication over
two sockets whenever I click on the sticky notes applet, so it appears to work.
I enabled verbose debugging with SIGUSR1.  This is what happens when I click on
the sticky notes applet when the visibility setting does not work:

Jul 12 21:33:41 perlas gconfd (mg-26115): Setting
/apps/stickynotes_applet/settings/visible in
xml:readonly:/etc/gconf/gconf.xml.mandatory
Jul 12 21:33:41 perlas gconfd (mg-26115): Setting
/apps/stickynotes_applet/settings/visible in xml:readwrite:/home/mg/.gconf
Jul 12 21:33:41 perlas gconfd (mg-26115):
/apps/stickynotes_applet/settings/visible was writable in
xml:readwrite:/home/mg/.gconf
Jul 12 21:33:41 perlas gconfd (mg-26115): Notified listener from-saved-state
(83886082) of change to key `/apps/stickynotes_applet/settings/visible'

This is what happens when I click on the applet after I restarted it and the
settings started to work again:

Jul 12 21:35:54 perlas gconfd (mg-26115): Setting
/apps/stickynotes_applet/settings/visible in
xml:readonly:/etc/gconf/gconf.xml.mandatory
Jul 12 21:35:54 perlas gconfd (mg-26115): Setting
/apps/stickynotes_applet/settings/visible in xml:readwrite:/home/mg/.gconf
Jul 12 21:35:54 perlas gconfd (mg-26115):
/apps/stickynotes_applet/settings/visible was writable in
xml:readwrite:/home/mg/.gconf
Jul 12 21:35:54 perlas gconfd (mg-26115): Notified listener stickynotes_applet
(234881033) of change to key `/apps/stickynotes_applet/settings/visible'
Jul 12 21:35:54 perlas gconfd (mg-26115): Notified listener from-saved-state
(83886082) of change to key `/apps/stickynotes_applet/settings/visible'
Jul 12 21:35:54 perlas gconfd (mg-26115): Received dir_exists request for
`/apps/stickynotes_applet/settings/visible'

It seems to me that gconf notification mechanism is broken, however I am not
familiar with the architecture of gconf.  It might be a bug somewhere else.
I would be glad to provide more information if someone could just point me in
the right direction for debugging this problem.