Why is java (32-bit) JDK installer not copying rt.jar file to JRE directory? (Windows 2008 R2 SP1)

The system is using Windows Server 2008 R2 SP1, Tomcat 5.5.28, and Java SE 6 Update 20 for both JDK and JRE.

I updated the system to the latest JDK update, Java SE 6 Update 27, and let it install using defaults; it created a new directory, jdk1.6.0_27, and overwrote the jre directory. It asked to restart and then I noticed Tomcat would not start. I ran the java -version from the jre directory and it outputted

Error occurred during initialization of VM java/lang/NoClassDefFoundError: java/lang/Object

I discovered the directory was missing the rt.jar file; I pasted it from the jdk1.6.0_27/jre/bin directory and java -version worked and Tomcat started. My question is why is this error occurring in the first plac开发者_JAVA百科e??? Is it the Java installer?

I ran the Java Automatic update feature (which only updates JRE, not JDK) and it worked without a hiccup. So, why is the Java installer from Oracle.com not updating the JRE directory properly?

Thank you in advance.

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I think that's the case all Windows installers have this obligatory phrase:

Please close all running programs before you continue with installation

I think something was holding the old rt.jar and installer has a bug that cannot cope with this condition.