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PDI Json input Error depending on Tomcat Run Mode

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I have a report based on a transformation that includes a Json Input step. This report and step seems to work correctly if the BI CE server has been run via the start-pentaho.bat (I'm on windows), but fails if the BI server is run under the Windows service as a jvm.
The Tomcat folder pentaho/WEB_INF/lib are identical so I don't think its that.
I have checked and their is a valid input Json as I can create a report which simply outputs the raw Json successfully.
The Json step seems to fail silently by simply no parsing the required field.
Any ideas about the potential cause of this?
Thanks

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