It's not only Software Updated. Unity on fresh 15.04 (amd64) doesn't see Oracle 
Fusion Middleware JDeveloper installer (java app) running. If you minimize all 
windows it's gone. Can be found with 
wmctrl -l

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https://bugs.launchpad.net/bugs/1003950

Title:
  launcher does not show minimized update manager while clicked

Status in Compiz:
  New
Status in Accelerated Xorg driver for nVidia cards:
  New
Status in Unity:
  Fix Released
Status in Unity 5.0 series:
  Fix Released
Status in Unity 6.0 series:
  Fix Released
Status in binary-driver-fglrx package in Ubuntu:
  New
Status in intel-linux-graphics-installer package in Ubuntu:
  New
Status in unity package in Ubuntu:
  Fix Released
Status in update-manager package in Ubuntu:
  Confirmed
Status in xserver-xorg-video-nouveau package in Ubuntu:
  New
Status in binary-driver-fglrx source package in Precise:
  New
Status in intel-linux-graphics-installer source package in Precise:
  New
Status in unity source package in Precise:
  Fix Released
Status in update-manager source package in Precise:
  Confirmed
Status in xserver-xorg-video-nouveau source package in Precise:
  New
Status in binary-driver-fglrx source package in Quantal:
  Invalid
Status in intel-linux-graphics-installer source package in Quantal:
  Invalid
Status in unity source package in Quantal:
  Fix Released
Status in update-manager source package in Quantal:
  Won't Fix
Status in xserver-xorg-video-nouveau source package in Quantal:
  Invalid

Bug description:
  Found an easy way to reproduce it during brussels sprint:
  1. start deja-dup or update-manager
  2. kill -9 compiz; metacity
  3. compiz --replace

  
  ===============

  Update manager is showing up in the dock but I can click on the icon
  all day and nothing happens. Similarly if I do Super-S or Super-W it
  doesn't show up anywhere.

  Even if I alt-tab to the application nothing shows up. This happens
  only when update manager runs on its own. If I kill it and then launch
  it myself it comes to the foreground just fine.

  I'm not 100% sure whether this is a unity, compiz, or update-manager
  bug but so far my bet is on unity.

  =====Original Report=====
  Bug #877444 is showing again in latest updates, please re-open it. This is 
the exact same problem.

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