Filemaker Server Admin Console & Java 6 Troubleshooting

So it appears that FileMaker Server 9 and FileMaker Server 9 Advanced sometimes don't play nicely with Java 6. In the past 24 hours, this has burned me twice. First, on the server side: I'm running FileMaker Server 9 Advanced on a Windows 2003-based server. FileMaker appeared to be fully patched and showed the current version as 9.0.3.325. After installing the latest Java Runtime Engine (which is