That upload fixes the problem:
control-center (1:2.17.90-0ubuntu2) feisty; urgency=low
.
* debian/patches/80_fix_user_directory_cleanup_when_no_autostart.patch:
- use xdg autostart dir instead of a gconf key non set by the package,
fix autostart removal cleaning the user directory when the corresponding
gconf key has no value (Ubuntu: #78500)
** Changed in: control-center (Ubuntu)
Status: Needs Info => Fix Released
** Bug watch added: GNOME Bug Tracker #402621
http://bugzilla.gnome.org/show_bug.cgi?id=402621
** Also affects: control-center (upstream) via
http://bugzilla.gnome.org/show_bug.cgi?id=402621
Importance: Unknown
Status: Unknown
--
gnome-control-center wipes out /home/user
https://launchpad.net/bugs/78500
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