Java commands are the Server Manager and Method Servers running when Windchill is started.
Are Windchill, Windchill DS and HTTPServer installed as services?
Are they set to autostart when the system is booted?
If they fail to start, check the log files for any error messages.
You can try to start them manually from their icons on the server desktop or start menu. Start Windchill DS first, then HTTPserver and finally Windchill. Open Task Manager and monitor CPU usage and memory usage. The CPU will get very high as the Method Servers start. Depending on your system speed, start-up could take 45-120 seconds, sometimes 180. CPU usage will drop to almost 0 when everything is up or the system crashes before being up. Watching the memory usage will tell if the system is up or crashed. The usage climbs slowly as each server starts and stays high if the system is up. If the system crashes, there will be a sudden drop in memory usage.