My problem, back in 2007, had to do with trying to change the proxy
networking settings. As I recall, everything else would work just fine.
My solution was to edit the synaptic configuration file manually.

Would you mind posting the contents of your synaptic configuration file?
There might be a clue there. It's a text file located at:

        /root/.synaptic/synaptic.conf

Additionally, you can try to re-install synaptic. You can do this from
the command line by typing in:

       sudo apt-get install synaptic dpkg

-- 
Synaptic Preferences Window hangs on clicking Ok or Apply
https://bugs.launchpad.net/bugs/174570
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