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There is a known issue when you use Xcode 4.5 and iOS SDK 6 to compile your app - the app would not rotate correctly. If you use Xcode 4.4.1 and the associated SDK, then rotation will work fine on both iOS 5 and 6 devices.
Xcode 4.5 certification should be coming soon - for now please try to use 4.4.
If you are already using 4.4, please let me know and perhaps there are configuration issues.