Eric, if your woodies bare shaft well, there's no reason for them to shoot worse than the carbons. When I have "bad" woods that I know are the right spine, it's usually a crooked nock. That will cause more problems with accuracy than anything else IMO.
You have to be sure that the woods all spine the same, within a few pounds, to get equal performance. If you don't have a spine tester, I recommend that you get one. Just because the supplier advertised matched shafts, that doesn't mean they actually are.
Another possibility is fletching clearance. If you know everything else is right, try turning the cock feather in. If it's a clearance problem, that should make a difference.