Please look in Documents/paradox/ck2/gfx/flags/ folder. There should be two .txt files and 3 or more .tga files there.
If there are no .tga files there, that is the problem. An antivirus app is getting in the way of the game creating those files. Avast and AVG are famous for this. Avast and AVg are th emost common causes.
Either you need to unload that AV app then run the game so it can make those files, or we have to make them separately. Sometimes users have installed the game on some other computer, let it make those files, and copy them across.
All the best!