I have slightly cheated but got it working. I reboot the NAS every night so not too worried if the thread is already running.

This is what I have done

in the Task Scheduler I have created a new user-defined script to run as admin and in the user-defined script box I have typed

/volume1/@appstore/JavaManager/Java/bin/java -Djava.awt.headless=true -jar /volume1/@appstore/jdownloader/JDownloader.jar &

This seems to be the main command from the S99jdownloader.sh file and successfully kicks it off for me.

thanks for the guide everyone