Using a configuration generated by xf86config, setxkbmap gives an error every time it is run that is something like (I don't want to go back to my old configuration right now, but this is based on my memory, enhanced by 'strings `which setxkbmap`'): Couldn't interpret _XKB_RULES_NAMES property The problem seems to be that xf86config generates a line at the end of the keyboard section like: XkbKeymap "xfree86(us)" whereas Xconfigurator, in that same place, generates: XkbKeycodes "xfree86" XkbTypes "default" XkbCompat "default" XkbSymbols "us(pc101)" XkbGeometry "pc" XkbRules "xfree86" XkbModel "pc101" XkbLayout "us" setxkbmap works like a charm when I change the first line (as generated by xf86config) to the above 8 (as generated by Xconfigurator).
don't use xf86config. We don't support it.