Thanks for this additional information.
Can you please give me the output of:
$ apt-config dump |grep -i MinAge
It looks like this is a race with the cleanup process for the debs in
/var/cache/apt/archives
** Changed in: update-manager (Ubuntu)
Target: None => later
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Feisty upgrade failed because packages vanished from /var/cache/apt/archives
https://bugs.launchpad.net/bugs/96664
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