The problem is that Synaptic caches the proxy settings in its config
file, and the "Apply system wide" option doesn't know how to replace
that (naturally).

Take a look in /root/.synaptic/synaptic.conf - I wager you will see the
old proxy settings. Either correct them there, or delete them so that
the global settings are used.

I'd suggest this is a bug in synaptic - it shouldn't cache proxy
settings that are obtained from the systemwide config.

-- 
Doesn't honor gnome proxy settings
https://bugs.launchpad.net/bugs/24250
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