I finally was able to reproduce it. Turns out it happens only once after
system startup, if I log out of the session and log in again, the bug is
gone.

Steps to reproduce:
-Make sure no desktop file manager runs in the session (eg. remove it from the 
session / xdg autostart locations)
-Start a gnome-flashback no effects session (Metacity)
-Wait for the desktop (appears empty due to no file manager)
-Run the 'nemo' file manager, set to overtake the desktop too
-The file window appears, the desktop icons too, but the are in front of the 
window.
-Close the window, the desktop appears to be normal
-Open any other application, it appears behind the icons again.
-Log out from the session
-Start a gnome-flashback no effects session again
-all is fine now.

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Packages, which is subscribed to metacity in Ubuntu.
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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