I have a UIViewController I created in my apps storyboard, as well as a custom UIViewController subclass which I added to the project (and is correctly in the compile phase
You can fix this by editing the XML of your Storyboard.
Right-click your My.storyboard entry in the Project Navigator panel and select the Open As->SourceCode menu choice. Find your view controller entry in the XML, and add the attribute customClass="MyController".
Save the storyboard.
Right-click your My.storyboard entry in the Project Navigator panel again, and select the Open As->Interface Builder - Storyboard menu choice.
The custom class entry will now contain your MyController class name.