So it seems that my issue was resolved by fixing the xorg.conf file. 
Amanda, Cory - If you want to upload your xorg.conf file (in /etc/X11 , it has 
no personal information) we can see if its the same issue that I had. You can 
also search the file for the words "mouse" and "keyboard" - if you find them in 
an un-commented line, it's probably the same issue.
Ubuntu guys, to summarize :
nvidia-xconfigure, "dpkg-reconfigure xserver-xorg" and (possibly the 
recover-X11 boot option) corrupts xorg.conf  (w.r.t. the mouse / keyboard)

Thanks,
Guy

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keyboard stops working in intrepid
https://bugs.launchpad.net/bugs/294791
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