Wow... peeking at dupes, it seems that authentication and non-proxy host
lists have been broken for years!!

Authenticated proxy is a very common requirement at large companies (I
work for a multi-national audio equipment manufacturer with ~10,000
employees, or so, worldwide for example), especially for filtering
content.  I won't say the name of the filtering software/server solution
because I don't want to give them any free advertising or kudos :-)

Anyway... this is going to manifest itself in lots of ways outside of
synaptic, and probably result in a LOT of weird duplicates on other
applications.  Worse, many apps (grip, picard, firefox, pidgin, etc...)
have their OWN proxy settings, so what happens is that the user ends up
configuring twenty different apps with their proxy authentication
information (which, by the way, is usually your corporate desktop user &
password!! so, yeah, fairly significant security worry there, too)
instead of the global proxy environment variable.  Not that an
environment variable with a password in plain-text is better security,
but at least it's only in one place...

I'll stop rambling now.  My point is that this bug may be somewhat
bigger than it looks, and frustrate people in unexpected ways, be aware.

-- 
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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