Comment 7 for bug 877088

I have the same problem. I had created my own (duplicate) bug for this problem at:
https://bugs.launchpad.net/ubuntu/+source/gnome-control-center/+bug/879223

I am behind a corporate firewall using a McAfee web gateway, a content-filtering proxy server. Our DNS resolves IP addresses without any proxy settings, but HTTP, HTTPS, and FTP connections cannot be made to addresses beyond the firewall unless we connect through the proxy server. So when executing apt-get, it resolves my mirror's IP address OK, but times-out trying to download the "Packages.gz" file. The only way to make "apt-get" work correctly is to set the "/etc/apt/apt.conf" file, which should be done by gnome-control-center, but it doesn't.

All I can do is write my own script to set "/etc/apt/apt.conf" to use the proxy, and execute it every time I want to run "apt-get" at the office.