It may be the machining of the bolt circle on the hub isn't perfect in relation to the axle. Axle may not be normal to the plane of the disc, or the hub mounts aren't all in the same plane. The outer nuts on the hub can be a little goofy as well. If you loosen the skewer and rotate the axle 90deg, then tighten the skewer back up, what does the disk look like when you spin the wheel?