OK, I can get the CMD to have a penalty. It shows up fine, but the Flat-footed value is not affected.
I do not know how to make it affect the FL value. This value shows up on the display while making your character, where the summary says "CMD # / FL #". I suppose that if it does not show up on the printout that it does not really matter.hero.child[Maneuver].field[tCMD].value -= 1