I'm not quite sure what you mean by "only two boxes show up". Can you attach a screenthot or a video showing this, and also let us know the site where this is happening?
When I'm on the b.c. website, I'm making a web app. When I add the for example, " Allow file upload" after checking the box, it isn't added after I save the web app. When I add it to a webpage, in the preview it doesn't show up, including some of the other boxes aka form boxes. I'll add the screen shoot.