Java Runtime Environment (JRE)
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A conflict may occur if one version of Java is installed natively and another one is included in a Thinstalled executable. This is because newer versions of Java also install a plugin DLL that gets loaded by IE. This plugin DLL overwrites virtual registry keys when it is loaded and can conflict with a virtualized copy of older Java runtimes. You can prevent IE from loading plugins by adding the following line to beginning of HKEY_LOCAL_MACHINE.txt

isolation_full HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Explorer\Browser Helper Objects