Hi, even I have had the same problem, in kde, starting synaptic from the menu, would bring up kdesu interface, after inserting the password, nothing happens, in my case the problem is metatheme (installed following this howto: http://fak3r.com/articles/2006/01/31/howto-mezzo-desktop-on-ubuntu)), infact issuing kdesu synaptic from comand line, resulted in no synaptic launch but it throwed me an enlightening error message:
MetaTheme error: Cannot load configuration file (/root/.metatheme/config).
I resolved the problem by copying the .metatheme directory from my user home to root's one:
me@mycomputer:~$ sudo cp -R .metatheme /root/.metatheme
Now, whenever I click on synaptic's icon in the menu, it correctly throws me the kdesu gui and after it starts synaptic! ^_^
So, my advice is to try kdesu synaptic, then look for the errors and try to fix them! ^_^
regards