I'm also having the same problem. I've added a third category that I want included on my navbar, but it's very difficult to select due to the whacked formatting.
I manage to select each of the categories I want by making the size of my browser window super-skinny, which stacks the check boxes on top of one another instead of tucking them behind eachother.
The problem is, once I select the categories, "Click to save category selection" and then Save Changes, the third category isn't added to my nav bar.
This is very frustrating, I'm looking foward to finding an answer!