We use the triple column layout and when running our app under Sequoia Beta, the Secondary view controller's navigation bar is not shown initially. If a view is pushed inside the secondary (which contains a UINavigationController), and then popped again, the navigation bar is shown.
Do you get the same results with just the relevant code in a small test project? If so, please share a link to your test project. That'll help us better understand what's going on. If you're not familiar with preparing a test project, take a look at Creating a test project.