I created an app in ios 6 with navigation view.Also I have set all orientation options in the application summary and even used the
-(BOOL) shouldAutoRotate
Phone apps traditionally don't support upside down (why would you hold the phone upside down?) - the default project will support portrait and both landscape options, but not upside down.
Change this in the project info viewer in Xcode and you should be fine. There is a visual representation of the supported orientations, and upside down will be unselected.