Excluding any antivirus or firewalls that may be blocking the SHUTDOWN port , make sure that there is a time gap between any start/shutdown/restart events of the Spotfire Server. Tomcat may take a while to shutdown all services and if the server is restarted immediately after a shutdown, it may not release all the ports. This can lead to errors during any later shutdown operations.
Based on the environment, make sure that the shutdown port is in listening mode (using netstat) before restarting the server.