Never mind. Wait long enough and let it chew enough ram and it gets there. Seems there are a few bugs.
The Always On section is under the Key Maps, which is partly why I called it the Always On keymap.
I see that your Toggle Formations Menu has different targets for both of the steps, and the way it is setup it will load the Formations menu on all game windows, but only unload it on the current window.
The default is to only load/unload on current window for both steps.
You can change this by selecting the step in question, and then the action within the step, and setting the Target to Window:Current.
Depending on which character set you load, you do have different settings.
On Character sets Copy of ConTroub and Copy of Controub1, these both have the formations menu assigned as part of the default startup.
To set the initial load state of menus, select your character set in the top left of ISBoxer, in the lower left, select Menus, and in the lower right, highlight the menus you want loaded to begin with, and unhighlight those menus you do not want loaded. You can always load menus on the fly with a Toggle setup, like the ones for the Toggle Formations Menu or Toggle Toggles Menu.
For character sets other than these two, It is possible that if you have previously loaded the Formations menu, then use the ISBoxer Ingame GUI to set menu positions and click Save, then the saved positions will save the formations menu position, and the reading of this file may cause the menu to load, even though it is not initially assigned (I've yet to test this whole thing out so this is conjecture). If this is the problem you can delete the saved position files for the menu. This will be in the Scripts subfolder of you Inner Space install. Usually C:\Program Files (x86)\InnerSpace\Scripts, and you can delete the ISBoxer.Menus.CHARACTERSET.CHARACTER.XML files (replace the character set/character values with the names of the ones you are having issues with).