I have the same problem using only the integrated graphics (HD Graphics 4600).
Starting Civilization V with DX11 in fullscreen makes my display (DELL U2414H) to switch from 1920x1080 to 1080i and showing screen flicker.
If I run it in Windowed-Mode it stays in the same 1920x1080 (p) mode like the desktop.
Starting Civilization V with DX9 the fullscreen mode works without any flicker, because it then runs in 1920x1080 (p) like the Desktop.