Disabled real-time protection: it might have to do with several reasons like faulty installations or incorrect/incomplete updates, etc. You might find clue in the Windows server application log among McLogEvents.
Autoupdate not finishing properly: "Unable to find a valid repository" means a lot of things regarding repositories, most likely: inaccessible repository/-ies, bad login information, repository content invalid, etc.
Update log can be found in a fle named McScript.log on the server. It is a bit detailed but can be tolerated. When you open it, look for the message "Unable to find a valid repository" and once you find it, scroll slowly backward and you might find the exact reason of this failure.
It is a good practice to always make sure %TEMP% folder exist and has proper free space, as this also can prevent updating from finishing.