A coupla things come to mind here, semi-floating rotor buttons tend to become non-floating pretty quickly! Causing the rotor to lock into a position that most likely ain't good. Thus your run-out.
Also calipers need to be positioned so the rotor runs through the caliper casting pretty close to the center of the casting. Otherwise you get a rotor that could be shaving the caliper at worst or just off-center so much that the pistons on one side are too far out of their bores (extended) while the other side is barely moving at all. Go look straight at the caliper from the front of the bike looking back and see if the rotor is shifted to one side or the other. Guarantee that just about all the bikes on this board will be off somewhat! This is a function of where the pinch/axle bolts are holding the bottom of the fork tubes, all it takes it one tip over or a wheel change where the mech did not bother to center the fork legs on the axle.
So.... lube the snot out of the carrier buttons and work them free with your hands, thus making them semi-floating again (very important).
Next... check that the rotor/wheel assy is centered in the caliper casting as above. This can be done by releasing the pressure in the hydraulic/brake system, loosening all the triple clamp bolts slightly as well as the axle and pinch bolts and re-tighten (using correct torque) everything so as to end up with a triple clamp > forks > axle > caliper/rotor alignment.
Fretka