Maybe this relates to the bug first described by #1538111. It seems
unrelated (all windows closing sometimes) but someone found out that the
windows are still open, yet hidden behind the dekstop background window.

So this matches almost the situation when the dekstop icons appear in
front. I just don't encounter the hidden windows because I do not use a
background image I guess (just set a solid color).

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https://bugs.launchpad.net/bugs/1614050

Title:
  Window depth order messed up

Status in metacity package in Ubuntu:
  New

Bug description:
  Using the gome-flashback session with metacity is totally messed up
  since I updated from Ubuntu 14.04.3 to 16.04.1.

  All the effects mentioned here do not appear when using compiz, so I
  guess Metacity is broken.

  -Windows that should open in front (like Kupfer) appear behind the
  windows already open.

  -Before nemo is run, the Ubuntu default desktop background image
  appear, it can't be changed by settings. I just guess this is due
  wrong ordering of the true background and some window used by Gnome
  for showing the selected background.

  -If nemo is run to take over the desktop, the destkop icons appear in
  front of all windows.

  
  I guess all those effects originate from a similiar reason. None of these 
problems where appearant at Ubuntu 14.04.

  This is a total show stopper for using metacity on 16.04 as everyday
  applications like nemo and Kupfer can't be used.

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