This is a problem I'm having only with the Linux test server build, on Windows it is working fine. When using the countdown timer via the messages.xml file for server restarts, when the countdown reaches zero it disconnects all players properly, but the server process itself does not terminate, it remains open indefinitely, so I'm unable to restart a new server process normally. I have to issue a kill command on the process to terminate it before restarting a new server process.
Also (this is very minor issue) the countdown display to clients is off by one minute, it states "Server will restart in 3 minutes...", then "Server will restart in 2 minutes...", then it says "Server will restart in 1 minutes.." and then instantly disconnects the client instead of waiting the 1 minute as it displays.
Also as others have reported, I sometimes get random crashes at around the 1 hour mark when players are connected, I've also seen the error "free() - corrupted unsorted chunks" reported in the console a few times.