You might check that you don't have two XF86Config files. The "old" XF86Config-4 and the "new" XF86Config file.
During transition from the old pre 4 XFree86, there was usage of the XF86Config-4 file but in recent XFree releases, the default config file is (generally) XF86Config. If you have two of the configs, the one that counts now is XF86Config. Copy and or remove XF86Config-4 and make sure that XF86Config is configured as needed.
Just a thought......