I installed the latest java and security updates (2009-001 1.0) to my 10.4.11 MacBook a couple of nights ago. Even during the installation process, it was showing signs of problems. The updater failed to install the update several times. The Macbook wouldn't shut down despite leaving it for 15-20 minutes. Nor would it boot. The only way to get the machine up and running was to do an Archive and Install.
Symptoms