I have the same problem with both of my bodies, in low light and trying to AF on fast-action. It boils down to the fact that I just don't think the 1DX's AF is as good as all the hype when it was first released
I believe this is true. The Ai Servo AF on 1Dx and 5D III does not seem to warrant all the initial hoopla, especially in Ai Servo. However, I just got my 5D MkIII back from Canon Service, where I had it cleaned and checked before the warranty ran out. I did mention to them that the Al Servo mode seems to have tendency to misfocus, and the service summary mentions:
"Confirm autofocus to factory standard (Ai Servo). It was found that the adjustment of the AF assembly was incorrect, causing the focus to operate improperly. Electrical adjustments were carried out on the AF assembly. Product function was confirmed."
There is no way to perform proper A-B testing of Ai Servo in exact same situation pre and post "AF adjustment," but I do believe the Al Servo focusing is working perceptibly better now, which is very difficult to quantify. If your recent Canon body is having unusually worse-than-expected Ai Servo performance, it may (or may not) be worth it to have Canon Service check it out before warranty runs out. They probably need a cleaning anyway..