The fix for CR 6643769 work differently in 5u17 and 6u11. In 5u17 the fix is comply with the behaviour described here (http://java.sun.com/javase/6/webnotes/trouble/TSG-Desktop/html/awt.html#gdaao section 2.7.5) while in 6u11 is not.
I can't reproduce this with 9. Browser behavior is different now, the test no longer opens popups but new tabs instead. It's unlikely this will be addressed anyways as applets are deprecated.