After a server crash, the server was automatically restarted. However, startup.sh didn't bring the Java Gateway back up again. It says "Zabbix Java Gateway is already running". It should start the service anyway replacing the stale pid file.

Shutdown.sh doesn't remove the pid file in case the process is not running either, it dies saying: .../shutdown.sh: line 8: kill: (20108) - No such process

So you cannot bring up the process with the means of these two scripts any more at all. You have to tease apart the script logic to find the pid file and manually remove it, but it's the case the system cannot stand up at it's own after a crash why I consider it as a bug.