Yes, this occurs as soon as I boot the game into the title. I was not using any of your other plugins in the process.
Windows.json is indeed created by SuperTools, it allows you to alter settings like columns, positions, and transparency of other windows used on the fly, and sits in the data folder alongside the maps and database stuff.
I was trying this as it's kind of troublesome getting a plugin that displays a map on the title to play nice with my other plugins (notably MV3D).