See my reply below. It definitely sounds like you're using system() (which returns) instead of exec() (which doesn't). Keep in mind that fork creates two identical processes, both running your perl script. Unless you want two copies of your script running, one of processes running your script must be overwritten using exec().

If the application you want to kill is started by your script, you might want to look into using Win32::Process module insted of fork. When you create an object, it returns an object with a ->kill() method.