The new server manager appears to have an issue with user name, specifically if it contains a space in the user name (windows not steam)
it will deploy the server but when trying to batch install mods or update mods it flags up an error stating it cannot read the script - c:\users\FIRST HALF OF NAME
it seems with a single name its not an issue and can batch install a collection of mods if the correct workshop id's are supplied in the modlist.txt file