Some server restarts with the messages.xml file don't always bring your server back up. The time is also normally off by over 15-20 minutes. For example if you have a restart message that restarts the server every 180 minutes, it'll restart around the ~190-200 minute mark normally. Occasionally the server will only stop, but never restart on it's own.
On occasion there is an issue where the nitrado web interface will say a server is up, but it won't appear on the server list. It has to be manually restarted again until "players #/#" Shows up on the interface.