Comment 26 for bug 365823

As far as I can tell by looking at the process tree, Synaptic gets run with gksu. When you click on it in the System menu, you need to enter your password, so it can run as root.
But! it is run by the user, from the user's home directory, and that doesn't change. You can check this by opening Synaptic, then in a terminal switching to root, doing a 'ps ax | grep synaptic', looking up the process ID (pid), cd'ing into /proc/<pid>, and doing a 'ls -la cwd' (which links to the current working directory), this should be /home/<user>.