CLS It's most likely got to do with the amount of centershot for the two bows. Once you get past ten yards however, those arrows most likely will show some variance in point of impact.
I'm with you on the bareshafting, I've never liked it. I tune with fletched arrows and broadheads. I also practice with broadheads and rarely ever shoot field points. All of my hunting arrows, especially woodies, have been individually shot and tuned to my bow. My last batch of Sitka spruce varied in finished length up to 1.25 inches in order to get good flight and same point of impact with brand new Zwickey Eskimos. There must have been alot of variance in the spine even though they were supposed to be 65-69# range.
I guess I would try bareshafting if I had to start from scratch with carbons. I'm sure it works. I'm just hard headed and prefer my own method.
Turpentine