The root menu entry Appearance -> Preferences Utility tries to launch the command /usr/local/GNUstep/WPrefs.app/WPrefs The path to WPrefs in the above command is wrong. It should be /usr/share/GNUstep/WPrefs.app/WPrefs with "share" replacing" local.
WindowMaker is now patched to install the adjusted WMRootMenu. Thanks for noticing the details. :) emerge rsync emerge WindowMaker
Version 1.4 on the LiveCD still has the same problem. Portage installs WPrefs in /usr/lib/GNUstep/apps/WPrefs.app/. WindowMaker is looking for WPrefs in /usr/share/GNUstep/WPrefs.app/