There was a thread a while ago about Reikan Focal in manual mode. It appears that cameras like the 1DX and 5D3 don't write into the Metadata wether AFMA was used when using back button focus and releasing the button before taking the picture, or at least they don't do it in a consistent way. They do still write the actual AFMA value into the Metadata, and they still do use AFMA. Neuro saw different information for his 1DX than I did on my 5D3.
I think it also depends on the software you use - I remember seeing a difference between different versions of GraphicConverter (which use different versions of EXIF Tool).
IIRC, there is a Exif tag AFMA ON 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, my camera wrote 2, which was interpreted as UNKNOWN, and most software seems to interpret that as OFF.
I have to go back and look at some of my shots for more details, or take some more test shots - I can let you know later today.
Bottom line is, your AFMA probably still works fine, the camera just writes inconclusive metadata when you use BBF.