Which autofocus are you using?

My is set on select but is in the center 90% of the time, when doing portrait mostly i shift it up one notch so that it focus on the eyes.
And I only use the AF button, not half press release.

When focusing on the eyes do you focus on the top of the nose or one eye?

It depends how the shot frames but mostly it's on the top of the nose yes. not truly perfect though but close enough if the dof is not too shallow.
If I've the time though, i only use the AF to move the focus close and then focus manual. My current most photograph subject is my little cousin of almost 2 so he does hardly sit still.

edit: had troubles with the family order.
Like John said you try to focus on the eyes yes, thought you asked me what I did. ^^;

On the eyes.

Thinking about it I suppose that when focusing in the centre and then re-composing, it makes sense to use centre focus, rather than letting the camera decide. Maybe that's where I've been going wrong

Be careful with re-composing, you are change the angle how you view the subject so if you move up to get a focus and then down, then that point in the center might be infront of the focus.

Not that it is bad just be careful when shooting with shallow DOF

Thanks for your answers and tips, I'll keep trying between manual and AF centre spot for the more difficult shots (sport & flying birds).

Selective point, mainly in the middle.