When Dragon Age Inquisition uploads "choices" to the Keep they do not upload your exact choices as what was chosen for that World State, you do in fact have to go through and correct all of that just like you did before. It will get close, but it will not be exact especially since not all choices are relevant to Inquisition.
The big thing here, is that they are based on your playthroughs, they are not exact. Meaning, if you had a female elven mage as Inquisitor that should match up, but which one of your Inquisitors will not necessarily be the right. The saved playthroughs are more randomized states close/similar to your imported and played state rather than being the exact and actual one. It's not something isolated to you, but it is because not all exact choices are saved via Inquisition rather the flags for the general/overall events are set.
So for example: You had Alistair as king, that means the Keep read it as any World State that at least had Alistair as king in the Ruler tile was acceptable for the playthrough World State.