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73416ba
(Get the code!)
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.