Also, you'll see two mirrors, one behind the main reflex mirror. The reflex mirror is transparent and it passes light to the AF mirror. That mirror reflects the light to the AF system on the bottom of the camera, and the sensors in the bottom detect contrast in the light.
The manual focus screen, as you may well know, is on the top of the mirror box right under the prism. In some Canon cameras (I know the 20D, 30D and 40D, I think the 350D and 400D as well, and I believe all of the 1/5 series) the superimposed AF point selectors and focus screen are separate. If you pull out your focus screen and look up under the screen, you'll see a transparent plate with boxes. If you don't, and the boxes are on your focus screen, then your camera has no superimposement plate. If the focus screen has no markings, the plate is separate. If the plate is gone or in incorrectly, or if your focus screen isn't in correctly, then you might not see the AF boxes flash in the viewfinder. If so, your camera may not be focusing where you want.
That said, try a focus test with a focus chart on all your lenses. Could be miscalibration.