Comment 26 for bug 24250

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.