You have to specify the path of the java bin folder in your batch file, otherwise the "java" command won't be found when executed in the QMC.
For instance, if you need to execute "example.jar" located in "C:\ExamplePath", you have to create a "example.bat" file in the same path with the following content:
SET java_path=C:\Program Files\Java\jre7\bin :: <your java bin folder>
"%java_path%\java.exe" -jar "example.jar"
Then in your QV script:
EXECUTE cmd.exe /C "C:\ExamplePath\example.bat";
Thank you, that seems to have done the trick - I still find this a bit strange because I set the whole Java environment up using the QMC service account and System Variables (JAVA_HOME, CLASSPATH etc..).
Anyway, putting the same variables and values in the batch file as suggested did the trick, so many thanks!