Is the thread out of pitch all the way down its length or is it just at the start for a few turns?
If the pitch error is at the start only :-
What can happen is the cutting load of the tool can stall the spindle for a split second and throw out the pitch.
Also you have to allow for acceleration of the tool, in most cases 6mm (1/4") depending on the spindle speed and reaction time of your machine, the heavier the saddle the more time allowed.
If its all the way down :-
Your machine calibration is out.
Graham.