My Camera Had Autofocus problems. Turns out, that against my previous knowledge, most of the sensors are not located on the actual mirror, but in the Sub-mirror, a smaller mirror behind the big one, that actually blocks the direct path of the shutter. My problem was focusing period. It would hunt to infinity on a lens, and then come all the way back (in USM, so pretty fast) to zero, to let me know it could not focus.
When it went back to Canon Repair Service, I spoke to the Pro Team there, and he explained that there are extremely tight specs -duh- for that submirror, that moves just as much as the real mirror does. They replaced the entire assembly, and it worked.
That is my experience.
I would suggest - for the sake of troubleshooting - that you switch the AF mode to manual, and that you then select the center point, and continue to test it. If AF works in one mode and not the other, then you have a situation you may cope with, realizing the focusing is somewhat impaired (as said above probly misaligned) and other AF points are more effective than others. Or, you may also notice the AF is pretty weak at its strongest point (dead center, single sensor). Then you can evaluate options for repair. The Replacement on a 1D Camera costed me about $195 less than a month ago.
Best of Luck,
HOSTED PHOTO
please log in to view hosted photos in full size.