Comment 15 for bug 949265

Did you try to investigate around su and sudo? Because gksu calls them regarding the option you passed (or not). In my case, the source of the problem is sudo.

By the way, I did manually set a root password in command line with "sudo passwd". Then I can connect as root in command line using "su" (with no option). Probably that's why "gsku -w -u root synaptic" works in my case...