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I have implemented a fix for this issue. I've added a field in the project fitnesse settings that will allow you to specify your JAVA_HOME for Fitnesse. If left blank, the default behavior is used (i.e. reference JAVA_HOME\bin\java.exe environment variable specifically and fall back on the command 'java' if it does not exist).
You can find the fork of this plugin at: https://github.com/Honesty-Box/fitnesse-plugin
The compiled fitnesse.hpi is also available if you don't want to build from source. Please be aware that the master branch that we forked had 3 failing unit tests for NPE in the class HudsonDependentTest.