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View Thread: Launching a SWT app in windows
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    Use javaw

    The javaw command is identical to java, except that with javaw there is no associated console window. Use javaw when you don't want a command prompt window to appear. The javaw launcher will, however, display a dialog box with error information if a launch fails for some reason.

    Also you can also prefix your command with "start" in your batch file to open up another console window.