In scratchbox, type "ls /etc/apt/apt.conf.d/"

See if there's one that says 90proxy, or something along those lines... it'll contain the word proxy, and start with 90-something (I don't know exactly anymore because I deleted it from my scratchbox!). If it's there, that's your problem... move it somewhere else, run apt-get update, and this time all should work as expected...