I found it ... D'OH The start/wait should not be there.
This is for one that runs all the time:
ECHO OFF
:UPDATE
Echo Updating
[your update command goes here]
:START
ECHO Starting Server
[your server startup command goes here]
GOTO UPDATE
When you type "exit" the batch file loops and starts again. That way you can update your server and restart it quickly.
.... and this is for the one you just start when you play then exit:
ECHO OFF
:UPDATE
Echo Updating
[your update command goes here]
:START
ECHO Starting Server
[your server startup command goes here]
Oh and take out the brackets ... this updates your server every time it starts ... it takes longer, but you dont have to " start it - stop it - update - start it ". The -autoupdate command only works on linux systems, not windows.