This issue occurs when you run Mendix from within you Eclipse. When you are stopping your Mx app by the debug 'Terminitate' button in Eclipse. And not via the console, it will keep running in the background. This will result in the errors above when you try to start up a other instance of the Mendix server.
Prevent it: Stop the Mx server via the Mendix console Log To solve it when it occurs: check in your task manager the running javaw.exe process of the Mendix app and kill it. (don't kill Eclipse it also runs with javaw.exe)
Cheers!