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.

-- 
Setting the network proxy doesn't change the synaptic proxy settings 
(gnome-network-preferences) for authenticated proxies
https://bugs.launchpad.net/bugs/300271
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