I've seen this happen a few times even when the headset and frame are perfect. If the headset spacers are carbon, they can vary in thickness from around the circumference, i've mic'd as much as a .005 difference side to side. Take a couple and stack them the right way and it adds up. The other thing I've seen is stems that have bad facing. My S-Works stem was off by a solid .010" out of the box and needed a little dressing up to make it square. Seen a few other 'high end' stems that were off too. That's usually the first place I look now, not the headset or cups.