This problem appears to be intermittent, but I am not sure why exactly. When running my application on the device (iPad), I have some code to load a scroll view with some image views according to the current device orientation. Even though the device is landscape before loading, the views are being loaded as if it were portrait.
The orientation is found by calling [[UIApplication sharedApplication] statusBarOrientation].
The views are set up to adjust their positions when the device is rotated, and indeed, rotating to portrait and then back to landscape returns them to the correct landscape positions. Is it the case that all applications start off in portrait and soon change to landscape if required? Am I trying to check the orientation too soon (during the init of the first view controller to be loaded)?
If you're subclassing UIWindow or the status bar you'll see this because that's the ipad device's native orientation. The UIWindow translates the orientation and coordinates into what we're used to. After you makeAndKeyVisible, your device and interface orientation in view controllers should be as expected. You wouldn't by chance be using MTStatusBarOverlay would you? I went through the same thing and it came down to the order of instatiation.