One of the Apple engineers has written the following about the problems.
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All,
We are aware of the QTJ + Panther Upgrade issue as it concerns Java, and will be providing steps to alleviate and prevent the problem shortly. We are still in the process of identifying every install configuration that is a problem, as well as possible solutions. Once that is done, we will make all the relevant information available, via the
http://developer.apple.com/java/ site.
Please keep an eye on
http://developer.apple.com/java/ for a statement on the problem described, who is affected, and what they will need to do.
md
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Matt Drance
Java Engineer
Apple Worldwide Developer Technical Support
dts@apple.com