The current version of Portage that is in Funtoo appears to have a bug (that may or may not be fixed upstream.) The basic issue is when an ebuild has this in it:

DEPEND=">=virtual/jdk-1.3"
RDEPEND=">=virtual/jre-1.3"

...the ebuild will attempt to pull in a JDK and JRE, even though virtual/jre's dep is satisfied by what is getting pulled in by virtual/jdk.

This isn't any good.