I have got the same problem using Xcode6 and I noticed that UINavigationItem is added automatically for the first ViewController that you embed into NavigationController but for the subsequent ViewControllers, you will have to add it manually as follows:
- In the Object library, find Navigation Item then drag it to your 2nd ViewController in the storyboard.
- In the Object library, find Bar Button Item then drag it the navigation item that you have created in the previous step.
Now you will have your Bar Buttons stuck to the top of your scene.
Update The solution still works with XCode 7 but I wanted to add more descriptive photo. Just in case anyone is not really familiar with standard or technical names mentioned above. Notice the red arrows in the right, they refer to step 1, step 2 mentioned above. Also note the hierarchy of views on the left red rectangle.