Hey guys,
I just found something that may help to solve the issue. I’m sorry for I should 
explain everything.

As you know it’s possible to change shortcuts keys from Dconf Editor,
CCSM, and also Unity Tweak Tool. Well, I’d tried both Dconf Editor and
CCSM, but the problem still existed. So I tried Unity Tweak Tool, and
yeah they does NOT change anymore. But the problem here is that Unity
Tweak Tool doesn’t have all the shortcuts.

So it seems the way the shortcuts are stored on home folder raises the
problem. Every time I changed the shortcuts, logout process would take
more than 2 minutes afterwards.

Some time later, my Ubuntu Unity Plugin got disabled by accident**. I just 
logged in and found it disabled. I had a blank desktop with wallpaper: no menu, 
no launcher. I opened CCSM and enabled the Unity Plugin. There were SOME 
CONFLICTS, the most important one for Show Desktop between Unity Plugin and 
General Options. I chose DISABLE for all. Wonderful! Both problems are solved 
now:
I have my shortcuts UNCHANGED after more than 10 reboots and some hard 
shutdowns due to power failure. Also the logout process is fast as always.

I conclude the problem is originated from the conflicts between (GNOME?)
General Options and Unity Plugin which both have settings to change
keyboard shortcuts.


** Not totally by accident. When logout process took long, I would kill 
X-server just by Ctrl+Alt+Backspace. The last time I didn’t kill X and waited, 
and opened DASH during the logout process! Maybe this caused Unity Plugin 
crashed on the next login.

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https://bugs.launchpad.net/bugs/1069053

Title:
  Keyboard shortcuts (System Settings > Keyboard) are reset to default
  values after  upgrading to 12.10

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