"As we mentioned in the previous section, it is best to establish nock location in accordance with the grain of the wood to take advantage of full spine weight. But if after shooting the finished arrows you find an arrow flight problem, the solution may be nock rotation. This may vary the spine weight slightly, but it is much easier than re-fletching your arrow shaft."
This is a quote off of an arrow shaft manufacturer's site. I find it interesting to see that they and others say that you may find that by rotating the shaft so that you find the stiffest alignment for the nock. I have always found that by placing the grain horizontally it is the stiffest. As the arrow comes around the riser it is bending against the grain. No need to rotate the shaft. Think about it...boards will bend with the grain easier than against the grain. That is one reason we build things with boards the way we do...right? But another important reason to align the nock properly is so the string is perpendicular to the grain. The force of the string is pushing against the grain not with the grain, which should help in stopping the shaft from fracturing along the weakest point...with the grain.