Cards placed in the add-on Section Boxes cannot be stored upright. You must tilt them. Or you could take scissors and cut a bit out from the top or bottom of the divider cards (I did this with Prototype 2 card dividers, but I sure would not want to do it with my final game). Here is the photo that illustrates what I am talking about:
Here was the question:
Here is the official response from AR-Jordan about needing to tilt the cards:
Both the cards and the dividers fit in the default Section boxes with their covers on.
What do the dividers actually separate?
Is it essential or just section cards from crew?
Prototype 2 had three dividers … Available Crew, Resting Crew, Section Cards