the issue was a libgksu one and fixed today
** Package changed: gnome-desktop (Ubuntu) => libgksu (Ubuntu)
** Changed in: libgksu (Ubuntu)
Importance: Undecided => Low
** Changed in: libgksu (Ubuntu)
Status: New => Fix Released
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Synaptic doesn't start in root mode
https://bugs.launchpad.net/bugs/394496
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