@dronus

check with some genuine config, to know if that still exist:
- purge compiz
- purge metacity
- set default theme (adwaita for ubuntu, does not know for others) via the 
tweak tool

- reinstall compiz (only the default ubuntu choice; no ccsm nor other plugins 
which are mainly not maintained since ages)
- reinstall metacity

- then logout and reboot;

note: set to "incomplete" as its not your report, and the OP has not
answered to #83

** Changed in: metacity (Ubuntu)
       Status: In Progress => Incomplete

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to metacity in Ubuntu.
https://bugs.launchpad.net/bugs/1538111

Title:
  untraceable serious bug in metacity 3.18

Status in metacity package in Ubuntu:
  Incomplete

Bug description:
  Ubuntu 16.04 LTS uses 3.18 version of gnome metacity.

  When doing lots of mess work in Desktop (such as open desktop window,
  sudo window, dragging window, and so on), "!! WHEN CLICKING CLOSE
  BUTTON OF A CERTAIN WINDOW !!", there is "small possibility" for
  metacity to get out of work --> Many windows are disappeared, with
  only nautilus desktop background and gnome-panel on screen. "Live
  Window List" still exists in gnome-panel, but no matter doing what
  (such as open new application from gnome-menu or use Alt+Tab to switch
  window), none of live windows can be displayed.

  So the only way is to switch to tty1 using Ctrl+Alt+F1, and executing
  "DISPLAY=:0 metacity -c --replace", then all windows came back.

  Till now, I meet this bug every day, but still not sure how to
  reproduce it bug. I think you should trace what the metacity do when
  clicking "close button" that makes all windows to be disappeared.

  Thanks.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: metacity 1:3.18.1-1ubuntu3
  ProcVersionSignature: Ubuntu 4.3.0-7.18-generic 4.3.3
  Uname: Linux 4.3.0-7-generic x86_64
  ApportVersion: 2.19.3-0ubuntu3
  Architecture: amd64
  CurrentDesktop: GNOME-Flashback:Unity
  Date: Tue Jan 26 19:49:48 2016
  SourcePackage: metacity
  UpgradeStatus: No upgrade log present (probably fresh install)

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