This is actually a 3.3.1 -> 3.5 upgrade question.
Ninja forms has been a great tool, but today I ran into upgrade problems. My client was on WordPress 3.3.1 and needed to upgrade to 3.5. So, we upgraded the plugins first. The Ninja Form upgrade resulted in the shortcode showing, instead of the form. The upgrade to WordPress resulted in the shortcode disappearing, but nothing showing. We have switched to Easy Contact Form in the interim, but the client really likes Ninja Forms, if we can get it going.