« on: December 07, 2013, 10:54:29 PM »
Canon technicians 'cannot figure out' the issue, because there isn't one, per se.
AFMA is engaged during focusing. If you've set up back button AF, and aren't holding down AF-ON, the camera is not actively focusing (which, in fact, is one of the main reasons to use back button AF). In that case, the AFMA isn't recorded in the EXIF as shown during on-camera image review or by DPP. It's always shown when AF is assigned to the shutter button (since a half-press precedes a full release, with AF on the shutter button, the camera will always be focusing when the shot is taken). In AI Servo, it's always focusing, too. If you try to view the selected AF point in DPP, you'll see an analogous issue.
Side note: the camera actually does write the actual AFMA value into the Metadata even with back button AF. In addition to the AFMA value, there is another EXIF tag for AFMA Status (or something like that) and it can have values like 0 (which is interpreted as OFF), 1 (ON), and 2 (UNKNOWN). In the scenario you describe, the 5DIII apparently writes a 2, which most software (including DPP, apparently) seems to interpret as OFF and doesn't display the AFMA value. Image editing software and many EXIF viewers don't even show the AFMA Status field.
The bottom line is that your selected AFMA is being applied to the shot, even if the EXIF doesn't show it. If you want to convince yourself, select a value that's way off (e.g., if it needs + something, set -20) and take a couple of shots in One Shot using back button AF as you normally do, and compare them to shots with the correct AFMA set - you'll see the -20 shots are misfocused, and the correctly set shots are sharp, even though none will show an AFMA in the EXIF.