I looked at your shot at 100% on flickr and it does look like it is focusing forward in the nose area (or at least at the front of the eye). Keep in mind, the camera is going to focus on the area with the highest contrast near the focus point shown. It does not focus on something in the little box... just close to it. In other words, the area it is looking at is bigger than the little fucus box that lights up red. Therefore, putting the spot on the back of the eye, is still going to focus on the front if it presents a higher contrast target in the same vacinity as the focal point indicator.

If you want the eye to have the best chance of being the object for the focal point, then do more of a profile shot and aim at the center of the eye. If the focus jumps to the edges of the eye, or something close, then the eye should still be in the DOF.

Having said that, you may want to see if you have a front focusing problem, because most of the shots that I have seen of yours seems to be focusing forward of what you are aiming at. This one seems to be focused on the front edge of the eye (highest contrast target) or even slightly forward of that on the nose which would be a low contrast area. If it is the front of the eye, then it is probably performing properly. If it is focused on the nose, then it would make me think it needs adjusting (which is not possible on your camera). If you bought a new lens and it is focusing off, then send the camera and lens to Canon, and have them adjust it. You spent enough money on the lens, and they should be willing to adjust it... or you can go through mutiple copies until you find one that works.

However, there are better targeting methods to testing focusing accuracy other than the frog. I would investigate those to see if you have a problem.

Pat