I succeeded in building Java3D several times in the past but I had to merge several projects together to avoid circular references and it worked. There should be no native in Java3D 1.6 as I removed the other pipelines not based on JOGL 2.
Sorry for the confusion, build.xml is the old version I have kept around as I find time to extract any remaining
pieces that are useful. build2.xml is what I actually use to build it. Check that the paths in build2.xml are
correct for you to find the appropriate jars, look for "vecmath.lib", "jogl.lib" and "gluegen.lib" in that file.