How to make a server with new UI

You could continue with Investigating, by renaming the CustomPluginVariables.JSON, player.JSON and Multiplayer.JSON, first one after the other, to get fresh ones generated, to see if a Setting in one of them causes the Problem and if that doesn't help, rename the whole UserData Folder and so on....
Or, as you've said, just use the Steam Command Dedicated Server, that already works for you, to save your Nerves and Time.

 

I could just copy them from the working install from steamcmd. I like getting the data so I can help others etc. Knowledge is power