As the description of Wscript:String value indicating the command line used to run the script: The command line should appear exactly as it would if you typed it at the comm
Take a look at the WSHSell object's run method. The following code works for me:
var shell = new ActiveXObject("WScript.Shell");
shell.run("cmd /c java -jar MyApplication.jar");
// should work without JARs as well, take care for the working path
The run method has an option to wait for the java program to return.
Hope this helps.