It seems in iOS 6, a drop shadow is automatically added to the navigation bar even when you set a custom background image. I\'m pretty sure this wasn\'t the case with iOS 5
I had the same problem and I've solved it by following:
CustomNavBar *navBar = (CustomNavBar *)self.navigationController.navigationBar;
[navBar setBackgroundImage:[UIImage imageNamed:@"navigation_bar_gray.png"] forBarMetrics:UIBarMetricsDefault];
navBar.shadowImage = [[UIImage alloc]init]; // this is what acctually removed the shadow under navigation bar