Tente usar o começo:
start java.exe -jar C:\GMSEC_API\bin\bolt.jar
start java.exe -cp "%APP_HOME%\lib\jython.jar;%APP_HOME%\lib\Hammer.jar;%APP_HOME%\lib\gmsecapi.jar;%APP_HOME%\examples\Python;%APP_HOME%\jython2.5.3\Lib;%CLASSPATH%" bridenstine.hammer.main.Main %*
Se você quiser que a janela permaneça aberta, use:
start cmd /k java.exe -jar C:\GMSEC_API\bin\bolt.jar
start cmd /k java.exe -cp "%APP_HOME%\lib\jython.jar;%APP_HOME%\lib\Hammer.jar;%APP_HOME%\lib\gmsecapi.jar;%APP_HOME%\examples\Python;%APP_HOME%\jython2.5.3\Lib;%CLASSPATH%" bridenstine.hammer.main.Main %*