I have the same problem. I have an Logitech MX500 mouse.
It switched the middle and right button with the standart xorg.conf (did a 
fresh dpgk-reconfigure xserver-xorg) and it is still switched after I followed 
this guide http://ubuntuforums.org/showthread.php?t=219894. I have also 
configured my graphic card.

** Attachment added: "/etc/X11/xorg.conf"
   http://librarian.launchpad.net/4938934/xorg.conf

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Right button and middle click on mouse are swapped
https://launchpad.net/bugs/68319

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