UPDATE - We found a fix:
I found the answer to our problem which as described below appeared to be exactly the same as yours. One of our other developers noticed an "unexpected nil in main window" when attempting to tap on the far right of the screen. This led me to do a new search and I found this thread on stackoverflow that actually contained the answer to our problem.
( here is the link to the question which help my answer: unexpected nil window in _UIApplicationHandleEventFromQueueEvent )
The actual answer came from frankish who suggested opening the main.xib (or main storyboard) and clicking on the Window in that and making sure that the "Visible at Launch" and "Full screen at Launch" properties are checked (set to true.)
In our case, it was JUST the "Full screen at Launch" property that needed to be set, but setting this fixed the rotation problem we were seeing AND it fixed an issue where when launching on iPad in landscape the far right of the screen was not touchable.
END UPDATE - (original non-answer below)
My answer isn't an answer, but I have run into the exact same issue. On rotate in our app, when building with Xcode 6, I see the exact same rendering issue as the the screenshots on this question. The exact same out of position rotate with black bars at the side and bottom. (Our app on iPhone doesn't support any rotation so we don't see the issue on iPhone. On iPad we support landscape left and landscape right. When rotating from one to the other, when the iPad does it's standard rotation animation, it will rotate out of position (showing the black bars) when going one way and then rotate back into proper position when going back to the other supported orientation. I don't believe it's related to any custom positioning or animation code. It happens with every screen, including the splash screen. It appears to be related to the built in Apple screen rotation. Obviously not every project has this issue in iOS but I have not come across the particulars that are causing this issue. I spent all day yesterday researching the issue and going through our code and I have nothing.
One piece of additional info. If I build with Xcode 6 and run on a device with iOS 7 then there is not issue. This issue ONLY happens when I build with Xcode 6 and run on a device with iOS 8.
Here is a link to my own question posted yesterday about this issue. (I did not come across this question until after I'd posted my question.)
Building project with Xcode 6 (iOS 8 SDK) causes landscape rotation rendering issue on iPad