I also get my best fletch clearence with a slightly high nock when bareshafting...but as was said it sounded pretty dang high in the orignal posters posts. The less the fletchings have to correct for the more accurate an arrow is going to fly.
Like I was saying, bare shafting atleast for me is just the beginning of tweaking a bow to perfection. SOme are easier then others. Some things just fall into synch. Either way get close here and the rest of your tuning will come quite easily!