Understood. Did another attempt. Let's see if it will work now on version 3.0.3.
I don't know if MK UI is designed to only work on scene menu or to build menus on every scene. But if it is supposed to only wotk on Menu Scenes, it seems to be pretty agressive with his changes. Because it changes and overwrites some functions of Window_Base without taking into consideration if the context is on a menu sce eor not. The result is that, Window_Base is also used outside of menu context. So every window seems to get be affected by his changes.
Hopefully this fix will do the trick now. Let me know.