I pinned the issue down (pun intended) and will leave it up to you to
determine whether this is a bug or not.

After looking through the update-manager source, I discovered the
markedKeep variable, and guess what:

>>> apt.Cache()['fglrx-control'].markedKeep
1

It turned out that I pinned it to an older version in synaptic, and
upgraded the package it with apt-get (which doesn't look at synaptics
pinning). I don't think update-manager should complain in this situation
though since the package is not upgradable.

-- 
Bogus 'the following updates will be skipped'
https://launchpad.net/bugs/55369

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