Hello Exculcius,
I have had quite a few problems trying to support iOS 5 and 6 together. One of my problems is that iOS 6 can automatically "initialize" a view controller in landscape (thus, no need to rotate it), where as in iOS 5, it will "initialize" the view controller in portrait only, then rotate to landscape if needed. I believe this is causing your issue. Although I am not completely sure if iOS 5 view controllers will "initialize" in landscape if the app is landscape only, as my apps usually support all orientations.
I haven't found an optimal solution to support both portrait and landscape while also supporting iOS 5 and 6. I have found a few work arounds that require the AppDelegate to wait for a very small delay (or wait until the first orientation change) and then correct the objects' orientations if necessary.
I think the first step would be to check the "status bar orientation" on load and after a short delay with iOS 5 and iOS 6 and figure out if there are any differences, maybe throw in a check for the view controller's orientation and the devices orientation just to be sure.
If iOS 5 and iOS 6 show different results, then I believe it is very similar to problems I have run into, and I will give you a snippet of my personal work around.
One question: Does your app only support landscape orientation and is the plist's UIInterfaceOrientation set to landscape also?
Also, in cases like these, I trust device's results over simulator results. So I suggest you test it on a device also.