Public bug reported:

Binary package hint: update-manager

update-manager no longer shows up in the systray when updates are
available in Xubuntu (Xubuntu has the pop up behavior disabled via gconf
key) . It does however show up, grayed out, when apt is running. Right
clicking and selecting show updates when it is in the systray shows the
available updates as expected.

** Affects: update-manager (Ubuntu)
     Importance: Undecided
         Status: New

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update-manager no longer shows up in systray when updates are available in 
Xubuntu
https://bugs.launchpad.net/bugs/551888
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