Here is some info from xwininfo before and after the hidden window is
corrected by wmctrl, hopefully someone can make use of it:

xwininfo -name 'Software Updater'

xwininfo: Window id: 0x3000008 "Software Updater"

  Absolute upper-left X:  2655
  Absolute upper-left Y:  380
  Relative upper-left X:  2655
  Relative upper-left Y:  380
  Width: 450
  Height: 319
  Depth: 24
  Visual: 0x23
  Visual Class: TrueColor
  Border width: 0
  Class: InputOutput
  Colormap: 0x20 (installed)
  Bit Gravity State: NorthWestGravity
  Window Gravity State: NorthWestGravity
  Backing Store State: NotUseful
  Save Under State: no
  Map State: IsUnMapped
  Override Redirect State: no
  Corners:  +2655+380  -735+380  -735-381  +2655-381
  -geometry 450x319+2655+380

10:59:27 [me@home] ~
wmctrl -R 'Software Updater'
11:01:28 [me@home] ~
xwininfo -name 'Software Updater'

xwininfo: Window id: 0x3000008 "Software Updater"

  Absolute upper-left X:  1078
  Absolute upper-left Y:  383
  Relative upper-left X:  0
  Relative upper-left Y:  0
  Width: 484
  Height: 116
  Depth: 24
  Visual: 0x23
  Visual Class: TrueColor
  Border width: 0
  Class: InputOutput
  Colormap: 0x20 (installed)
  Bit Gravity State: NorthWestGravity
  Window Gravity State: NorthWestGravity
  Backing Store State: NotUseful
  Save Under State: no
  Map State: IsViewable
  Override Redirect State: no
  Corners:  +1078+383  -2278+383  -2278-581  +1078-581
  -geometry 484x116+1068+345

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You received this bug notification because you are a member of Ubuntu
Touch seeded packages, which is subscribed to unity in Ubuntu.
https://bugs.launchpad.net/bugs/1003950

Title:
  launcher does not show minimized update manager while clicked

Status in Unity:
  Fix Released
Status in Unity 5.0 series:
  Fix Released
Status in Unity 6.0 series:
  Fix Released
Status in “unity” package in Ubuntu:
  Fix Released
Status in “update-manager” package in Ubuntu:
  Confirmed
Status in “unity” source package in Precise:
  Fix Released
Status in “update-manager” source package in Precise:
  Confirmed
Status in “unity” source package in Quantal:
  Fix Released
Status in “update-manager” source package in Quantal:
  Confirmed

Bug description:
  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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