Your first problem is that you're using version 1.08.
1.10 fixes a few bugs and issues that you're going to be complaining about sooner or later.
You're first issue is that you have auto-start enabled in the server manager and you're also manually starting the server when it crashes. Uncheck the auto-start option untill you get the server up and running.
The port problem is also stemming from the fact that you have the server auto-starting when it crashes. When you manually start it after it has auto-started it think's you're trying to start another server on the same ports.
You need to find out why the server crashed in the first place. Were you running shipped maps when the server crashed or mod maps? What's the location (path) of the server manager when you run it?