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I am experiencing the same issue with all versions of the Java updater. Well, actually I only tested the updaters after .25. But the issue exists with them as well. Run the Java updater which says a reboot is required. After the reboot some of the Java files are missing and Java does not work. Have to uninstall Java and reinstall.
What I find odd is that I've never had to reboot my machine to complete a Java installation. Perhaps that is because I always install the runtime through the JDK installation and not through java.com?