If I understand the problem correctly, you are focussing with the central area and then moving the camera to recompose. That's your problem. This technique has been proposed time after time, but it is flawed.
The lens tries to focus with a flat plane; if you move the camera, that point on which you focussed is no longer in the same plane. Jonathan has a link to his site where he explains the effect with a diagram that makes it very clear.
Without a diagram, think of it this way:
1. take a T-square and put the end of the long straight part to your eye and look along it as with a rifle, placing your subject at the junction of the two parts of the T-square;
2. the plane of sharp focus is represented by the straight line running along the short piece;
3. move the T-square as if to re-compose and you will see that the straight line of focussed space no longer flows through the point you originally focussed upon. That point now appears closer to the camera so you will inevitably be focussing beyond it;
4. say that original focus point was six feet away - it still will be six feet away when you re-compose, but will only be in focus if the lens is describing a circular zone of sharp focus which renders all subjects six feet away as sharp. The lens actually makes a different, flat sharp zone which stretches sideways from the point on which the centre of the frame is focussed right out to a sideways infinity.
In essence, you are depending on a curved zone of sharp focus when what you really get is a flat one parallel to the back of the camera. Focussing on one plane and then moving the camera changes the whole dynamic and will never work.
Rob C