the necessary config files don't get install for sun java jdk not that there are 1.3.1.02 and 1.3.1.03 ebuilds. i tried to get a work around, but i'm running out of time right now. if i get a chance i'll look into it later basically the /etc/env.d/java/20sun-jdk* files are not getting created.
in /usr/portage/dev-java/sun-jdk/files copy sun-jdk-1.3.1 to sun-jdk-1.3.1.03, and re-emerge. (same probably works for sun-jdk-1.3.1.02)
Fixed in CVS.