Given all this informations, it seems that the DB is generated too early
(when APT hasn't updated it cache yet) or without internet connection at
all. The desktop isos bring some cache files with them, so there is no
issue.

I would even bet, this issue is present on old alternates, too.

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https://bugs.launchpad.net/bugs/1446830

Title:
  can't find uninstalled packages on a system installed with the
  alternate image

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