You can close this bug. Turns out apt doesn't like going through
Dansguardian. The PC with Ubuntu is behind my firewall with a
transparent Dansguardian proxy. Even configuring it to manually use the
Dansguardian proxy breaks it. Configuring synaptic/apt to use squid
directly however solves the problem.

Sorry.

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apt-get update looking for files that don't exist
https://bugs.launchpad.net/bugs/235246
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