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Position Tolernace not working

I have a cylindrical feature that is designated as a true position from datum F and datum B on a drawing. My part is aligned to so that the z plane is my A datum, my x plane is my B datum and have created a plane which represent the F datum. When I set up the part and input all necessary information for my cylinder feature everything works properly and the part measures within the specified limits. When the program is executed for my inspection the part no longer is in spec when measured to the required datums. Any ideas or is more information needed?