Public bug reported:

Binary package hint: gnome-system-tools

Some applications (all of the command line and some others like synaptic) are 
unaffected if you choose "Automated configuration of proxy" (not sure on the 
exact text, i don't use the English version) in proxy settings. 
If i use the "Manual configuration", those applications work but i cannot 
access some website. The solution, as i found by sheer luck, is to set the 
manual settings to apply system wide first THEN set the automated 
configuration. But if you don't know there is little chance you'll ever find 
the solution.

There is two possible solutions to this :
1-Make it so all the applications can use "Automated configuration of proxy" 
(Hard i think)
2-Give only two choices : Direct or Configuration (The current manual 
configuration) but add an option (checkbox) to "Use automated configuration 
file for application that support it".

I think option 2 could be done easily and would at least not let the
user search for hour why he cannot access Internet with some important
applications.

** Affects: gnome-system-tools (Ubuntu)
     Importance: Undecided
         Status: New

-- 
Proxy auto-config (PAC) not usable by some applications
https://bugs.launchpad.net/bugs/587097
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