I too was a bit worried about the focusing prowess of the 1DX. Tried to manually AFMA, just as bad... Then I picked up FoCal and spent a weekend tuning all my lenses. Now, focus hit and it hits accurate.
For reasons I cannot explain, the 1DX seems to be much more sensitive to needing accurate AFMA settings than the 5DII. If I might hypothesize, I would say the focus is so much more accurate than previous systems that if your lenses are not tuned to the body, you will get poor results. The 5DII seemed to be more about luck with focusing, the 1DX is about precision.