I had this problem as well. It turns out that you need to leave Street Atlas in 'window' mode (Non maximized) prior to using it within the shell of MEdia Engine. Just run Street Atlas from Windows and click the window mode in the upper right corner and than close Street Atlas.

Not exactly intuitive, but I guess Media Image can't control everything! Seems to me that there is a command line switch within Windows that allow you to open an application in non-maximized mode, but I haven't researched this.

Future thought: When opening a third party app for GPS like Street Atlas, it would be great if the music control buttons could be put at the bottom of the screen so that more of the screen is used/usable by the GPS application.