Bisch,
If you tune your arrows, and get good flight at those settings, I don't think it could be a flaw.
The reason we generally use a higher nock point for 3 under is because that's where we get good bare shaft flight. I think the reason behind that is that we will get good bare shaft flight when we are pulling at a point where both limbs bend equally. Since the force of our fingers is applied at a lower point on the string with 3 under, we have to move the nock point up some so the center of force is still at a point on the string that causes the limbs to bend equally.
I have heard of people who don't have to use a higher nock point when they shoot 3 under, and my theory is that they apply most of their pressure on the top finger. Could it be that you apply more pressure on the lower two fingers, rather than split between the first two fingers?
In a further note to Scoobiedooo, there is a great deal of latitude in raising the nock point higher, but not much latitude in lowering it. If you raise the nock point, the arrow will come off the shelf high, but the feathers will immediately correct it. A lot of people like to use a 1/2" nock point for split in order to avoid any possible bounce off the shelf, even though they might get by with 3/8".