Those updates were likely phasing
(http://www.murraytwins.com/blog/?p=127) at the time and apt is not
aware of the phasing percentage so will install all available packages,
while update-manager / update-notifier is and will not install all the
available updates.
** Changed in: update-manager (Ubuntu)
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1387177
Title:
Is not updating all packages
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