I just had the same situation.
I happend when one package during the upgrade failed to configure.
Update-manager returned to its screen and reported one available update
in the header without showing anything in the treeview. After
closing/reopening update-manager it reported (correctly) that there is a
borken package.
** Changed in: update-manager (Ubuntu)
Importance: Undecided => Low
Status: Needs Info => Confirmed
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After installing all possible updates update-manager still shows amount of
available updates
https://launchpad.net/bugs/89676
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