When opening a new menu with Disable Menus Underneath on, the new menu will disable the prefab of the previous menu instead of its instance in the scene.
This only happens to the first menu, like the start menu, other menus behave correctly.
How to recreate:
1.Set up two menus with MenuSystem.
2.Open the first menu on startup.
3.Open the second menu with Disable Menus Underneath on, using a button on the first menu.
4.You will see that the prefab of the first menu is disabled, but the instance in the scene is still active.