1. As I can make out from your query, you've updated the options related to Microsoft VM in the Internet Explorer, Tools -> Internet options -> Advanced. Changing these options should not make visible difference during normal operations. The following are the options you see:
i) Java console enabled: is only useful for testing of web Java programs - relevant if you're a web site designer.
ii) Java logging enabled: just creates a log of Java activities. Relevant and useful for debugging your java based web pages and also for managing/tracking security.
iii) JIT compiler enabled: A compilation mechanism for java programs in the web pages.
2. If you want to completely disable Java, go to Tools ->Internet Options -> Security. Click the Custom Level button, scroll down the list, and locate Microsoft VM - Java Permissions.Select Disable Java. This will disable Microsoft VM.
3. If you also have the Sun JVM, you'll see a section Java (Sun) in Tools -> Internet Options -> Advanced Tab. If a Microsoft JVM is also available, there is a section called Microsoft VM. To enable Sun's Java, turn on the checkbox labeled Use Java 2 v1.5.xxx for <applet>.
4. Even when the Sun JVM is being used, in the Microsoft VM section, the option for the JIT compiler (ref. 1-iii above) remains selected. Also, under the Custom Level of the Security tab (ref 2 above), the Microsoft VM section remains with High Safety selected. It is advised that you don't change Java permissions to Disable Java option - it most probably will disable the Sun JVM also!
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