Jeff,
Just because you tuned with FP's does not necessarily mean you will be tuned when you go to BH's. If when you were bare shaft tuning and using FP's you were able to dial them in perfectly, that is, the bare shafts were impacting exactly with the fletched shafts all the way out to, say.....25 yds, then there is a very high likelihood that when you switch to BH's your shafts will be too stiff, assuming they are cut the same. Also, remember that if you are using BH's that must be hand sharpened,then you need to do all your BH tuning with BH's that have been file to the same weight.
Brett