I just upgraded to Xcode 5.1, and when I open my project again, something happened with the 4-inch iPhone layout.
Now it fits only 3 inches.
When a 4-inch device / simulator displays only a 3.5-inch layout, this is a sign that you forgot to include the 4-inch launcher image in your project. Runtime uses a startup image to decide whether to display 4 inches on a 4 inch device.