I have since fixed the problem with some help from members of the
ubuntuforums.org community. The way I fixed it was by typing these lines
into my Xorg.conf file in the mouse section:

Option          "Buttons"               "7"
Option          "ButtonMapping" "1 3 2 8 9"

Having the 3 and the 2 switched brought my mouse buttons into the
correct order so that all functions worked as they should. Also oddly
enough installing Beryl and XGL fixed the problem also. Under XGL my
buttons are fine, in regular Gnome my buttons were mixed up.

For reference my mouse is a Logitech mx518 wired mouse. I followed a
guide to setup the side buttons a long time ago that I found on
ubuntuforums.org so that  could possibly be part of the problem. I undid
everything I modified from that guide though and still had the problem.

My xorg.conf file is attached. Currently it has code in it for the evdev
driver so that I can use my side buttons on my mx518. The original
section for the mouse is still in there though, it's just commented out.
In the regular mouse section you will also see the fix I mentioned
earlier. Thanks.


** Attachment added: "xorg.conf file"
   http://librarian.launchpad.net/4967354/xorg.conf

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

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