This is fixed in the current edgy. Proxy settings in gnome-preferences will be picked up via gnome- terminal/gksu and the apt proxy settings will be honored too from the update-manager/dist-upgrader.
Cheers,
Michael
** Changed in: update-manager (Ubuntu)
Status: Unconfirmed => Fix Released
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Dist upgrade detection does use proxy
https://launchpad.net/bugs/46290
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