I've updated Xcode to Xcode 7. Then my Swift project to Swift 2. At last I removed removed all warnings.
Everything was fine on previous version of Xcode. On Xcode 7, LaunchImage does not display on simulator for iOS 9 but display for iOS 8.
All places are filled on assets: remember it work well on iOS8.
Try unset LaunchImage, save, then reset LaunchImage.
If the issue is still there, you can try recreate your xcodeproj.