I've bareshaft tuned hundreds of bows, and the only times I've seen nocking points this high was with short recurves that were designed for an elevated rest.
Also, it's possible to tune for decent arrow flight when the arrows are too weak by raising the nocking point. I suggest trying some stiffer arrows, or reduce point weight to see if that helps.
You mentioned that you didn't have the spine tuned in- you really need to get the spine right before you can get the nocking point right. If that doesn't help, I agree with James- there's something wrong with the bow.