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EVALUATION
This problem is specific to new generation plugin only. Java5 doesn't contain new generation plugin.
SubCR for Java 5 has been filed by mistake. I'm closing it.
On Java 5 Oracle is experiencing CR 6743056 which is a similar but not the same problem.
Test case is exactly the same for both 6743056 and 6809648.
The difference between 6743056 and 6809648 is that for 6743056 browser freezes *before* user clicks OK button on Java Script alert window and for 6809648 browser freezes *after* user clicks OK button on Java Script alert window.