In "Top Activities" and in the DisplayList view, Scout says that the time is spent "Copying to Screen". This is normally a very quick operation where flash copies its back buffer to the display. My first recomendation would be try this using a release player. The second is to try it in a browser. Standalone and debug players can perform quite differently. Also check in Session Info to confirm that the runtime version is correct. I think what you are seeing is "Waiting for GPU" time as "Copying to Screen". You are probably just blocking on the GPU for VSYNC. That is normal in many cases and usually shows up as gray Inactive time.
To be specific ... make sure you are using the latest runtime: Flash 11.5 or Air 3.5.