When you compose & focus via the viewfinder, the dual-pixel system isn't used. The shutter has to be open (and the mirror has to swing clear of the image path) in order to use the dual-pixel system.
The standard phase-detect AF sensors are on the floor of the camera. Hiding behind the reflex mirror is a smaller secondary mirror. The primary mirror is semi-transparent to allow some light to bounce through to the secondary mirror -- and then down into the AF sensors. The path is measured so that the distance straight through to the sensor, vs. the distance to the focusing screen, vs. the distance to the phase-detect sensors are all the same (and the mirror is shimmed at the factor for this.)
When the phase-detect AF sensors detect that the image is "out of phase" at a particular point that should be focused, it measures how far out and also reads the direction of the phase shift (to know if it needs to bring focus in closer vs. out farther.) It then sends the corretive movement to the lens which, if carried out correctly, will EXACTLY bring the image back into phase in just ONE adjustment (it does not "hunt" for focus.) The amount of focus correction will depend on specifically which lens is attached to the camera. It is possible for the focus correction needed for one lens to be fractionally different than the focus correction needed for a different lens (not just a different type of lens... even a different copy of the same lens model.) This is why AFMA is cool... you can tune the AF system for your specific lenses.
It is ALSO possible for gears to wear, get loose, and develop "backlash" (gear slop). Suppose the last focus motion was to bring focus in closer -- but now the camera needs to send focus out farther. The first tiny bit of movement (that the camera thinks would be moving the lens elements) is really just eating up some of the backlash in the gears (the lens elements aren't really moving yet.) This can throw off the accuracy of contrast-detect AF in a somewhat random way and cause inconsistent focus (so inconsistent that even AFMA cannot compensate for it.) Continuously re-focusing would eventually refine the focus, but if if you've got lenses with backlash in the focus gears then that lens needs a tune-up (it's a lens problem, not a camera problem. Moving that same lens to a different camera body would still exhibit the same problem.)
Hopefully you are happy with your new 5D III... but if it has focus problems, either you need to apply some AFMA (use a proper commercial focus test chart... do NOT use ordinary pictures to judge focus accuracy) or possibly you have a lens (or lenses) that could benefit from a tune-up.
Tim Campbell
5D III, 5D IV, 60Da
