Comment 4 for bug 300271

If you are referring to gnome-network-preferences, that's what I used to set the proxy and proxy exceptions settings. This is supposed to write some variables which other programs use (amongst which, I suppose, synaptic, but also things like wget), in /etc/environment.

When you change the settings using gnome-network-preferences (and use the set system wide button), some variables are not written to /etc/environment, namely the ones that govern the authentication for the proxy, and the exceptions list. The ones that say which server to use are written to that file. This has the effect that an effected app either can access the proxy server but can't authenticate, or that it can access a proxy server that doesn't use authentication, but doesn't know when NOT to use the proxy, eg when accessing stuff on the local LAN.

Steps to reproduce:
1) open gnome-network-preferences
2) select manual configuration, enter a valid proxy server, set up authentication if needed
3) add some exceptions on the next tab
4) click set system wide, fill in password
5) check /etc/environment: observe that the settings for the proxy are there, except the ones for authentication, and the no_proxy one.