So you've found the missing file. The question now is why it isn't being picked up by the server. I would assume it's not being picked up because of some JMX reason, maybe your JMX username nad password are incorrect in the server editor?
When you run from the command line, does the shutdown script work if you type ./shutdown.bat -S -u admin -p admin ? (Use different username / passwords according to your config of course, but make sure htese match what you'll find in the server editor)