I'm pretty new to dconf, so I'm making some assumptions which may be
incorrect.  When dconf update is run as root, that only updates settings
which are either mandatory or defaults system-wide.  Neither of those
changes should result in a change in the users home directory, and if a
user wasn't logged in, nothing would happen currently.  Because of that,
I'm not sure that dconf update should be sending any signals which would
trigger a gconf sync.  At most, it should just re-read the system
settings in order to accept the new default or mandatory settings.  Even
if that doesn't happen, on next login, they will be re-read, right?

Unrelated, I'm surprised to find dconf defaults that don't match up with
gconf defaults.  Like the metacity button_layout dconf default puts the
buttons back on the right.  This was the primary reason I noticed this
was all happening in the first place.  when dconf update ran, it updated
the gconf setting for the button layout and moved the buttons back the
the right.

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https://bugs.launchpad.net/bugs/1071950

Title:
  gnome-settings-daemon dconf to gconf plugin causes settings to be lost

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