The launcher's tooltips state that EE cannot be used with the alpha mod, and some scripts will not work when EE is active. What is the "alpha mod," and what functions are approximately disabled?
Scripts don't work on RPG maps, or in the Unicorn Empire campaign (this is currently poorly controlled in the game, but in future versions, these scenarios will not be displayed in the game). Dynamic groups also don't work, but this is controlled by the launcher, and they cannot be enabled simultaneously.