I've had no focusing issues with my 1D2. Could you give some more details about how you are using the camera (sports, landscape, PJ, etc), focusing mode, and lenses used?
Are there consistent circumstances/conditions under which you have focusing problems?
Also, are you letting the camera select the focus point or are you choosing youself?
There may be back or front-focusing issues . If you search here on these keywords, you should find simple ways to test for this.
Paul