Synaptic uses in that order: its own settings, apt settings defined in 
/etc/apt/ , then the environment. 
It's a bit tricky to sort, because synaptic must be run as root to install 
packages and can't easily access the gconf setting for the user who launched 
synaptic. furthermore, if the user and root have different proxy setting (user 
settings not applied system wide), then synaptic will behave differently 
whether you're running it as a user or as root and it may create more confusion.
I've something in progress but which need more work.

-- 
get proxy config from gnome configuration
https://bugs.launchpad.net/bugs/13661
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