Focusing

After one week of shooting with the Phase One 645AF and the Leaf Aptus II-6 I have to say that i am very pleased with it. The picture quality is beautiful and it is really fun to shoot. However, im having a big problem with focusing. It seems like the only way to get the focal point excatly where I want it is to manually focus the lens. The problem is that manually focusing or auto focusing, the image can look correct through the view finder and on the digital back,  but once I get it into the computer its pretty far off. Here are some examples:

As you can see in this image, the focus point was on the dogs face. I didnt move at all but when I got the photo into the computer, the point of focus was on the handle of the leash. 

As you can see in this image, the focus point was on the dogs face. I didnt move at all but when I got the photo into the computer, the point of focus was on the handle of the leash. 

In this image the focus point was on the speakers face but the shot was actually focused on the items on the table. 

In this image the focus point was on the speakers face but the shot was actually focused on the items on the table. 

In most of the portraits I take, I try to get the very center of the focus circle over the pupil of the eye but it wants to focus on the nose.

In most of the portraits I take, I try to get the very center of the focus circle over the pupil of the eye but it wants to focus on the nose.

This is a big problem for me cause I feel like every shot is a gamble and I cant trust the camera to focus where Im telling it to focus. I really need to find out if there is a way to pinpoint the point of focus in the center of the focus frame(see red crosshairs below).

Any tips, advice, trouble shooting help would be awesome. Thanks!!