What else do I need to do to install the latest version?
It is because you probably (almost definitely) have TypeScript plugin for visual studio installed. You can uninstall that from Control Panel. Then the typescript you installed from npm will be the default one on the command line.
Alternatively you can get the latest TypeScript from Visual Studio 2012 plugin from here : http://www.typescriptlang.org/#Download (For VS 2013 it is bundled as a part of VS 2013 update 2 RC)