It looks like the problem is this: initially, apt clears the "Marked"
flag from all packages.  When aptitude tells apt, on startup, to upgrade
a particular package, apt notices that the package isn't marked and
figures it must be unused, so it sets the package back to manual mode.

  Arguably apt should be using the Garbage flag (which starts out false)
to check that, but I can work around many cases by just initializing the
Marked flags before I set initial states.  I don't know if this will fix
100% of observed problems, but it should fix most of the ones reported
in this bug.

  Daniel


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