I have duplicated this in the 64-bit versions of Xubuntu 13.04 and Ubuntu Server 13.04, so I believe the problem is in xfce4.
1. Go to settings / window manager / keyboard.
2. Set "<Super>q" as the shortcut for close window. Test, it works (close windows by holding the "super/command/Windows" key and pressing the letter "q."
The key combination no longer works for closing windows. Go to the window manager settings again, and you will see that "<Super>q" is still set. The config file does not appear to be altered, either:
Clicking on the option and manually hitting the key combination to set it again apparently does nothing -- it does not visually change the setting -- but the command now once again works for closing windows. Until the next reboot.
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