NFHS legal windup

[SMEngmann]

I am a coach and a basketball official. I am unclear about an apparent rules difference between the NFHS and the NCAA regarding legal action from the windup. My pitcher was called for an illegal pitch because he engaged the rubber with his hands seperate and then he brought his hands together snd paused and was called for an illegal pitch and charged with a ball. Is this ruling correct, and if so, what is the rule reference. I know NCAA Rule 9-1 (a, 1, c) states that it is legal in college, and I don't see any conceivable reason why the rule prohibiting this in HS should exist. Am I missing something?