There are lots of reasons that this could be happening.
One reason,
You are setting flash lock exposure on the subject by pointing the AF point or box at the subject (person). Your flash is throttling back so as to not over expose the person.
Try bouncing the light of the ceiling. Youll find that the background will be better lit and the lighting on your subject will be more natural.
Are you shooting in auto, aV, TV??????, Can you post an example of the pic in question, it will be easier to assess what is happening.