I only see one thing in the log that mentions the console and it appears to line up with a bug in vanilla, according to the bug report it is because the game tries to read commands from the command line as well as the GUI Console. This problem should not affect the server if you start it with the nogui flag like in the bat I suggested, if you can give up the prettiness of the GUI a cmd window will give you pretty much everything you need to know (/list will give you a list of players whenever you get curious)