I just installed synaptic (KDE-December) and launched it from K-menu. The window asking for root pw opens first, this window belongs to Policykit1-KDE I think. So do you have the right stuff like policykit-1 and polkit-kde-1 installed?
The command used in K-menu (as seen in menueditor) is 'synaptic-pkexec', and that also works from Alt+F2 krunner. Launching synaptic from homerunner-kicker works, too.