I have experienced this "wicked" behaviour when setting up firewall
rules on a machine connecting to the Internet through a DSL modem. I
believe that I have found a fix but I'm not completely certain.

The following conditions apply:

Clean install of Ubuntu 10.10
FreeNX installed per instructions on https://help.ubuntu.com/community/FreeNX
Guarddog 2.6.0 installed

The following seems to have fixed it for now:

Allow http(s) served from the internet zone to local zone (required by apt-get.)
Allow DNS served from the internet zone to the local zone (for remote DNS 
server.)
Allow DNS served from the intranet zone (192.168.1.0/24) to local zone (for the 
DSL modem's DNS server.)
Allow SSH served from the local zone to the intranet zone (for FreeNX.)
Enable DHCP on local Ethernet adapter. 

Hope this helps too!

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https://bugs.launchpad.net/bugs/574886

Title:
  Apt has strange network errors when updating indexes.

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