With changes in namespaces and project clean up and CMS.PortalControls was moved to CMS.PortalEngine.Web.UI. Without error it is hard to tell where exactly is the call coming from.
Is this an upgraded project or some custom code file? It is possible, that some references were not changed.
Have you tried clearing temporary .net files? Same cached files from older version could have been loaded instead of new files.
You can check web config for direct assembly references and lastly you can try clearing global assembly cache as well to ensure new assemblies are loaded.