[botmeister]

Yes, paused = Yes will prevent a server from starting. You'd normally want to keep all the servers paused except for one when you have more than one server config in the ini.

You are right about the .bat files. When a reboot happens there's no memory of which server config was last in use.

There is a way around this, it is still a bit convoluted but perhaps easier than editing the ini file each time. You could have more than one ini file stored as templates in another folder. Each template is configured to match the settings specified by a corresponding .bat file. When a .bat file is run, it copies the corresponding ini template file over to the serverloader install folder, which will overwrite the existing one with the template. The next time the server is restarted, it will load whatever was the last copied ini file, which loads whatever server was last specified by running the .bat file.