something similar has occured in my lenovo y500 laptop.
mouse clicks close/minimise windows but do not open panel menus or any other 
icon. even pressing enter doesn't open selected icons. i logout and log 
back(CTRL + ALT + BSPC) in to make it all right. this has happened while 
changing the volume in vlc or using the super key for the water effect of 
compiz-fusion or while the laptop was idle for a while.
here's what my xorg.conf looks like

sam...@sameer-laptop:~$ cat /etc/X11/xorg.conf
# xorg.conf (X.Org X Window System server configuration file)
#
# This file was generated by dexconf, the Debian X Configuration tool, using
# values from the debconf database.
#
# Edit this file with caution, and see the xorg.conf manual page.
# (Type "man xorg.conf" at the shell prompt.)
#
# This file is automatically updated on xserver-xorg package upgrades *only*
# if it has not been modified since the last upgrade of the xserver-xorg
# package.
#
# Note that some configuration settings that could be done previously
# in this file, now are automatically configured by the server and settings
# here are ignored.
#
# If you have edited this file but would like it to be automatically updated
# again, run the following command:
# sudo dpkg-reconfigure -phigh xserver-xorg

Section "Device"
Identifier "Configured Video Device"
EndSection

Section "Monitor"
Identifier "Configured Monitor"
EndSection

Section "Screen"
Identifier "Default Screen"
Monitor "Configured Monitor"
Device "Configured Video Device"
EndSection

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Losing keyboard and mouse control when changing screen brightness with fn + 
arrow under intrepid
https://bugs.launchpad.net/bugs/285323
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