I finally had some more time to look at this, and it actually is working as intended, more or less.
When Preset 2nd Press is set to IA, pressing a preset button activates the IA function underneath. The preset button changes to the button's "IA on" color to indicate that the IA is turned on. Pressing it a 3rd time switches the IA function off and returns the button to the preset button's normal color.
You have IA actions underneath the preset buttons that select Axe-Fx scenes. When the Axe-Fx changes scenes, any IA button that selects that scene automatically turns on. So the IA underneath the preset button turns on and its color shows through.
To disable this, you can remove the scene IAs underneath the preset buttons, as I mentioned above. Or, you can do one of the following:
- Set the IA on color to black - this tells it to not change the button color when the IA is activated
- Or, you can add another action at the top of the list. The GT only looks at the first action in a button's list when searching for scene buttons. If you have something like a Macro action that calls an empty macro in the first position, it won't try to do anything with the button when a scene change happens.