Does it work if you wrap it with:
Mmmm no luck with the wrap :(
Have you tried the "Send Event" scriptstep with the "do script" option instead of the native applescript? I don't know if this will work but it may be worth a shot.
"do script tells FileMaker Pro to perform a script in the language of the target application. Click Specify Application to select an application, and use Document to select the document to use with the target application. Or, select Script text and enter script text or type in the name of the script (make sure it is one that will be recognized by the target program"
Ok I have managed to sort this issue out by adding "unset JAVA_JVM_VERSIONS" ie do shell script "unset JAVA_JVM_VERSIONS; /Library/Java/Home/bin/java -jar /Applications/dcm4che-1.4.32/bin/hl7snd.jar mllp://10.0.0.2:2575 /Applications/dcm4che-1.4.32/bin/worklist/file.txt"
This works a treat!