When setting JAVA_HOME for gcj-jdk 4.6.3-r2 in a gentoo prefix, the PREFIX is ignored. i.e. $ java-config -g JAVA_HOME /usr/lib/gcj-jdk-4.6.3 when it should return /home/jeff/amd64-linux/usr/lib/gcj-jdk-4.6.3 The package is otherwise installed correctly, as far as I can tell.
Fixed, you will have to reinstall to get the fixed env file. Thanks for the report. 13 Jan 2013; Ralph Sennhauser <sera@gentoo.org> files/gcj-jdk.env: Make vm env file Prefix aware. #445350