I can confirm this behaviour on two entirely different laptops, both installed 
pre-release and then upgraded to final quantal.
Creating a new user does not help in any way.

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https://bugs.launchpad.net/bugs/955955

Title:
  Keyboard shortcuts get reset at every login

Status in “gnome-session” package in Ubuntu:
  Confirmed

Bug description:
  I have two sets of keyboard shortcuts that I change from the defaults:
  - ALT-T to open a terminal
  - ALT-<N> to switch to workspace <N>

  In unity 3d, when I logout and then login again, they no longer work. I go to 
the keyboard shortcut preferences, and they are still there. To get them to 
work again, I have to:
  - disable the shortcut with the backspace key
  - set it again to my desired value

  Then it works as long as I don't logout again.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: unity 5.6.0-0ubuntu4
  ProcVersionSignature: Ubuntu 3.2.0-18.29-generic-pae 3.2.9
  Uname: Linux 3.2.0-18-generic-pae i686
  ApportVersion: 1.94.1-0ubuntu2
  Architecture: i386
  CompizPlugins: 
[core,composite,opengl,decor,mousepoll,vpswitch,regex,animation,snap,expo,move,compiztoolbox,place,grid,imgpng,gnomecompat,wall,ezoom,workarounds,resize,fade,unitymtgrabhandles,scale,session,unityshell]
  Date: Thu Mar 15 09:27:44 2012
  InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Alpha i386 
(20120201.2)
  ProcEnviron:
   LANGUAGE=en_US:en
   TERM=xterm
   PATH=(custom, user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: unity
  UpgradeStatus: No upgrade log present (probably fresh install)

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