That didn't occur to me. Yes, I am testing this on a saved file.
I'll make some test maps and try it on a new game file and see if that changes anything. (at work right now though)
I'm also using a script call command to call the menu.
I'm using Eli.MapSelect.callScene()
I'm only using plugin commands when adding new maps. This bug still happens when calling the menu through a script call in an event when there are innate maps set up in the plug in parameters.