Quote Originally Posted by neuroanatomist View Post
Correct - autofocus (and AFMA) is always done with the lens wide open. It gets stopped down to the selected aperture just before the shutter is opened.
Which is why AFMA will not help you correct for focus shift at different apertures, as some certain pesky lenses seem to have (even expensive ones).

Still, we've gone from 1 AFMA value for a whole zoom lens to 2 values, long and wide end, and from per lens-type to per-serial-number.
In the future I don't see it impossible that you could dial in different values for different apertures too, it's just a matter of canon getting off their butts and coding it in (and maybe a bit more nvram for a huge lookup table), and a lot more work for us testing at every possible combination...