I found out the reason, but I don't know how to reproduce the bug.

Sometimes, metacity failed to recognize depth layer of "nautilus/nemo-
background" and normal window, see the following ->


When I get trapped into this bug described above, running "killalll
nautilus" under tty1 (Ctrl+F1), then all window except nautilus
background can be seen !!!!!!!!!!!!!!!!!!! It seems that metacity thinks
nautilus background has higher layer than normal windows.


I don't think it's the bug from nautilus, because of the following proof:


1) even replacing nautilus with other similar file explorer like nemo, this bug 
also happens;

2) when using compiz or older version of metacity, this bug don't
happen;


So I think there should be some check of source code that is related with the 
top-level window  covering other window. Don't let nautilus background (nemo 
-n) cover all normal windows.

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

Title:
  untraceable serious bug in metacity 3.18

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