I found that there was a bug with Starbound where my character got soft locked out of the server by being falsely flagged as already logged in. In these situations you are able to make a new character and re join the server, but there is a chance that starting up the single player with your soft locked character will remove them from the server and allow you to rejoin. So to clarify. If you get the "already logged in" bug, start up single player as that character and spend at least 5 minutes faffing around. Then try to re join the server.