have you (OP) Figured this problem out? I finally figured it out on mine a few days ago...
Login as root.
Run xf86config from a terminal
Choose all your hardware from the lists that will eventually pop up
Once it saves, if it is like mine, it will save as 'XF86Config' under one of the two directories mentioned above.
The problem for me was that XF was reading settings from a file called 'XF86Config-4' instead of 'XF86Config'
Just cd into the directory of the config files.
then cp XF86Config-4 XF86Config-4.old to back up your old settings
then cp XF86Config XF86Config-4 to copy the settings that were made with the config tool to the file that XF actually reads from when it loads.