java keeps running until the application ends. If you call it from a shortcut, it opens a command box which won't close until the application ends.
javaw starts the application in a separate process, then exits immediately. If you call it from a shortcut, there won't be a command box. It should usually only be used with GUI (AWT/Swing/SWT/...) applications, because you can't interact with any command line application nor see its output.
So what is probably happening with your .bat file is that it is a command line application, and you don't see the command box like you're used to.