There are tools/applications to reconfigure keyboard related files. Helps to know which Linux distribution you are using in order to point you in the right direction though.
Most if not all modern Linux distributions don't run xfree86 no more, they now use xorg.
Below is my Debian Lenny keyboard section of /etc/X11/xorg.conf:
Identifier "Generic Keyboard"
Option "XkbRules" "xorg"
Option "XkbModel" "pc104"
Option "XkbLayout" "us"
Since mine is pretty much like yours, I'm guessing your problem is not with the xorg.conf file. My Lenny has nothing in the /var/lib/xkb/ folder also, but it's not running right now, I looked at it from Mandriva which has three files in that folder but are named with a bunch of random digits.
Do you have a problem with the keyboard or is it working alright?
Is the error still there after a reboot? I'm wondering if these files are generated at boot time.