You should make absolutely sure you imported properly from the keep, and that you are not using a default world state. The choices of the default state can be found here:
http://dragonage.wikia.com/wiki/Dragon_Age_Keep#Default_World_State
In the default state, Alistair and Anora ruled together, so the odds are you did not import properly.
I have read some claim DAI correctly imported most decisions from the Keep but had a couple crucial errors, though usually this revolves around Hawke. Unfortunately there is no other way to know if your world state imported correctly other than verifying the time stamp at import, and checking the lore entries in the codex and listening to what people have to say about the history of the world.
The world state cannot be altered mid-game, you can only start another game to correct your world state.
