I don't have any that are supposed to add scroll bars to any arbitrary window, but maybe there is some kind of weird conflict going on. I was afraid of that. I'll do some testing by disabling some plugins.
Figured it out. For some reason, there is a collision with Yanfly message backlog. It's rendering the backlog window's grey transparent background and scroll bar on the menus created by your plugin. Truly odd. I'll see if I can figure out a workaround.
Alright, it's a little sub optimal but works fine for my purposes. Changing the render mode of the Yanfly message backlog window from "Dim" to "Window" and disabling the scrollbar option cleans up the screen.
Disabling and forcing the event system to create only base windows that might break the menu system on MV when using that plugin. At least a workaround exists for now (temporary)