Hi Jonathan
Your problem is unfortunately very common (see the 1Ds forum at http://www.robgalbraith.com/bins/index.asp - and here in the archive, I believe - for details).
You should bring your camera and lenses into CPS and get them calibrated when you're back at base. First you should test the focus. Print out this scale:
http://www.lewisohn.co.uk/scale45.jpg
tape it on a wall and shoot it at 45 degrees, focussing on the central bar. You should do this at different distances from the scale, as any back or front focussing will be exaggerated the farther you are from the subject.
This will show if your camera/lens combination is back or front focussing. Both the body and lens can be tweaked by Canon, but I understand there are only 7 'settings' for the lens calibration (a lens that was slightly backfocussing came back from CPS frontfocussing slightly).
Two more things to bear in mind. Make sure the diopter on the eyepiece is set to your vision, and once it is, tape it down (it should definitely be lockable; it is very easy to move inadvertently).
I'm sure you're aware of this, but it is important not to focus on your subject's eyes two thirds up the frame using, say, the central focussing point and then recompose. If you're shooting with a wide aperture, it will be out of focus.
There's a new, and very welcome, Canon PDF outlining this issue, as well as many examples of getting the most from the camera's custom functions at. see this page from the link to the download page:
http://www.robgalbraith.com/bins/content_page.asp?cid=7-6460-7335
Finally, I for one find the 1Ds viewfinder very difficult to 'trust'. It is so small compared to an RZ's. And I certainly agree that shots that look in focus through the viewfinder sometimes aren't.
Until you get back from your job, I would focus manually.
Good luck!
Richard Lewisohn
http://www.lewisohn.co.uk
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