Additional to B H answer. Also look this answer.
Got this issue when launching my landscape only app from portrait orientation (also the app shouldn’t be presented in recently opened apps list, which can be seen by pressing Home button twice. Perhaps, iOS somehow caches the orientation and window size).
My code was
self.window = [[UIWindow alloc] initWithFrame:[[UIScreen mainScreen] bounds]];
[self.window makeKeyAndVisible];
I set W+H autoresizing mask for window, it didn’t help me, because the window don’t being resized on rotation, but the transform matrix is changed.
The solution is simple
self.window = [UIWindow new];
[self.window makeKeyAndVisible];
self.window.frame = [[UIScreen mainScreen] bounds];
So the frame is set AFTER the window get its orientation from root view controller.