Is your problem that you have a packaged IE and Java locally installed? And with this setup the Java will not work for the packaged IE?

If this is the case it sounds like the registry in your IE package is using full isolation modes and parts in the registry where Java tells IE that it exists. Finding all keys needed to be made visible to the package might be quite hard but possible.

On way to find out what is needed would be to package Java as a ThinApp and investigate the registry such package creates.

If I misunderstood you and you simply need to create a package with IE and Java it should be much easier.. We have a couple of blog posts discussing IE and Java. Please look through them all.

http://blogs.vmware.com/thinapp/internet-explorer/
http://blogs.vmware.com/thinapp/2008/10/step-by-step-in.html
http://blogs.vmware.com/thinapp/2010/01/step-by-step-instructions-on-how-to-thinapp-newer-java-versions.html

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