This Canon EOS-1D X AFMA Bug update just in from John:
"With AF4 menu option Orientation Linked AF Point set to the default of Same for Both Vert/Horiz, behavior of the AFMA setting is normal. But, when it's set to Select Separate AF Points (which mine was), the AFMA zeroing out occurs."
"Simply changing that one setting from default 'breaks' the AFMA behavior ... and resetting that one setting to default restores the correct behavior."
"Trowski figured this out, also."