I embedded a navigation controller in a tab bar controller, the problem is that the navigation bar (with the blue color) get under the status bar. So the status bar appear transparent because it shows what is under. Here is a screenshot:

I tried to modify the status bar directly in Attributes Inspector to black and Translucent black, also disabled autolayout although i know it has nothing to do with such issue. Anyway, nothing is fixed. I used to work with that in iOS5, but since iOS6 and the new 4″ storyboard screen, i got this issue.
There is a misunderstanding here. The navigation bar is not “under” the status bar. This is iOS 6’s new color-adopting status bar. You can read more here.
If you do not like this behavior, your only option is to make the status bar black. Take a look at the project properties page.