Sun Microsystems was an early backer of the AMD64 architecture, back when it was still a bold move to support AMD for server class hardware. Not surprisingly, SUN offers AMD64 builds of the Java JDK and JRE. The actual JDK runs great, but the AMD64 versions are inexplicably missing some critical desktop pieces. The browser plugin is not included with the AMD64 JDK. Also missing in the AMD64 JDK is java webstart functionality.
AMD64 Plugin Support is one of the top 5 requests on Sun’s issue tracker. The issue was originally submitted THREE YEARS AGO.