I am building with the release version of Xcode 7.0. No storyboards, just nib files.
I have a single UINavigationController created by the app delegate
UINavigationController
I solved this by moving some of my code to viewDidAppear. If I used UIAlertController, it would cause the same problem you mentioned and would not be displayed, and I solved it the same way.
viewDidAppear
UIAlertController
Let me know if that doesn't work!