I also noticed a related problem that update-manager has with proxy-settings.
I'm using approx for package-caching on a central server and therefore have 
specialized sources.list files on my clients. On my Laptop I have Hardy 
installed, apt is configured correctly and manual invocations of it work 
perfectly, as does synaptic.
Only the update-manager insists on connecting to my approx server via port 
3128, but I cannot find out where it gets this idea from. $HTTP_PROXY is empty, 
and the only application that even knows about squid running on the same 
server, is Firefox. Of course, as soon as I stop squid there, update-manager 
here fails and reports a refused connection.
Since I couldn't find out why it always tries port 3128 (or even tries to use a 
proxy at all), I even purged and freshly installed the package, but still the 
same behaviour.

After all I found a very interesting solution:
Synaptic offers an option to activate and configure a proxy. Of course the 
settings were empty and disabled, but I intentionally filled in the settings 
for my squid (same server as approx, but port 3128), clicked on "accept" and 
immediately afterwards changed this setting to "direct connection" again. 
Clicked on "Accept" once more and voila, update-manager connected correctly via 
port 9999...

So I suppose it's rather a bug in Synaptic than in update-manager which
obviously takes this information somewhere from synaptic. Strange
though, that synaptic itself must have kept this setting from sometimes
earlier, but did not use it in this wrong way anymore.

Best Regards,
Fredl.

-- 
update-manager connects to obsolete proxy
https://bugs.launchpad.net/bugs/183750
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