There is a scene in Iron Man 3 when Colonel Rhodes is holding up a bunch of guys in a building somewhere when Tony calls him and asks something like "AIM did the software for"Your re-design, your suitbig re-brand, that was AIM, right?" and Colonel Rhodes replies "Yea, that's right""Yeah". So if AIM did the redesign and updated the software for the suit, then chances are Killian put in a override in the suits software to prevent the wearer from being able to control it.