It's reproduceable for me. However, it's not the icon that's not
transparent (the icon is, at /usr/share/icons/hicolor/16x16/apps
/updates-notifier.png); it's the widget that it's on. Note also that the
problem isn't update-manager, it's update-notifier, so we're attached to
the wrong package here.

-- 
Icon update-manager not transparent
https://launchpad.net/bugs/94171

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