This is completely puzzling me, I am using Xcode 6.4 and iOS 8.4 and the iPhone 6 simulator. I start a new vie controller project for the iPhone only, go to the main storyboard turn off auto layout, keep size class data for iPhone, and disable Size Classes. I then put down four UIStepper one in each corner of the view in the main storyboard. The build and run the app in the iPhone 6 simulator.
I have also tried cleaning the build folder and starting a new project altogether but this keeps happening. any suggestions would greatly be appreciated.
The picture shows the results being offset left and upwards.

Have you tried to run it in an iPhone 5s simulator? For me it looks like that your Storyboard is configured for an iPhone 5s display.
However I would not recommend you to develop without Auto Layout and Size Classes, because your App will not work on different iPhones and thus probably will be never in the App Store.
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