I think the problem is that EA didnīt add flags to many teams.
In the demo if you play with Real Madrid you didnīt see any flags but if you choose Juventus you could see the flags.
So the places for them in the stadiums are there but the textures are not.
I dont have the game yet but if you play at San Siro with AC Milan you will see flags. Try playing with AC Milan in other stadiums.
If my theory is right you will see the flags.
But donīt worry, I have collected tons of flags since fifa07 and PES and i plan to convert them all to FIFA11-
Just wait until i get the game tomorrow (my birthday) and the release of the first tools and I will start converting.