That header section is called global navigation and was added last year to help improve site navigation. In the 'Get Started' section of the Global Navigation: New Ways to Get Around and Brand your Sites with ArcGIS Hub and ArcGIS Enterprise ... article they highlight how to turn on/off the global navigation.
Thanks for the instructions. In Portal for ArcGIS 11.0, the Global Navigation option is under Settings > Interactions. However, it doesn't remove the header from an app that is opened from the Gallery Card.