While this bug don't happen very often to me, it behaves exactly as
described.

Some clarifications:

-It is not linked to Nvidia graphics, but happens on Intel too.

-It is definetely about graphical window depth order. The "hidden"
applications can be focused and work as expected. They even change the
mouse cursor according to their actions. They are just obscured by the
nautlilus or nemo desktop.

-If nautilus or nemo is killed, all other applications reappear, until
nautlilus or nemo is run again, in which case they are obscured again.
This can be repeated reliable after the bug once triggered.

-If metacity is restarted, the bug is gone until it is triggered again
by unknown reason. Trigger is likely the apperance of a new window (I
had the bug triggered on the failing appearance of some delete
verification request dialog).

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https://bugs.launchpad.net/bugs/1538111

Title:
  untraceable serious bug in metacity 3.18

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