Have you tried using the focus points to the left and right of the selected AF point. It would help to see samples and know what custom functions you have set. It is really hard to comment without seeing the photos in the sequence. Reset all the custom functions to default and try setting up the custom functions again.
I set my Custom Functions to this with the exception of leaving safety shift off and changing the Tracking sensitivity based on the subject, Haven't found a sweet spot yet for that.
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