On a Citrix environment 2 different applications were required. One of the applications required java version 1.5 (and didn’t work with 1.6) and the other application needed specifically version 1.6.

Because the applications are installed on a Citrix server the users do not have write permissions to HKEY_LOCAL_MACHINE so that was another complication.

After a lot of monitoring with process monitor the general process of how a particular Java version loads in Internet Explorer became clear to me.

Java adds an addon to IE called ssv.dll, you can see this trough Tools | Manage Add-ons | Enable or Disable Add-ons:

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