Do you run dapper? And use gnome-terminal? The gnome-terminal in dapper will 
automatically set the http_proxy environment. Apt-get uses this environment to 
get the proxy configuration. If you use a different terminal or no X at all, 
you have to configure it by different means (e.g. setting http_proxy by hand). 
There is little we can do about this because apt-get runs as the root user and 
it cant connect to the calling users gconf settings.

Cheers,
 Michael

** Changed in: gnome-control-center (Ubuntu)
       Status: Confirmed => Needs Info

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proxy configuration is confusing
https://launchpad.net/bugs/43747

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