I have two viewControllers, one is a subclass of UIViewController (autoresizes correctly), the other one is a subclass of a subclass of UIViewController.
I did a layout in I
I ran into this before and it was incredibly frustrating. It turns out that when you have Simulated User Interface Elements turned on then you can't change the struts and springs like you want.
Go to Attributes tab (Cmd-1) and make sure that Status Bar, Top Bar, Bottom Bar, and Split View are all set to "Unspecified." Then go back to the Size tab (Cmd-3) and you'll be able to click the lines and changes your Struts and Springs. Then finally you can go back to Cmd-1 and turn those simulated elements back on.