an error on line 100 in dev-java/icedtea6-9999.ebuild causes ./configure to search for rhino in an invalid location. line 100 should look something like this instead: rhino_jar=$(java-pkg_getjar rhino:1.6 js.jar); else you end up with: --with-rhino="--with-rhino=/path/to/js.jar" which makes baby jebus cry.
This looks fixed now.