I've unlocked several quests in the book but the crafting recipes aren't available. I don't just mean in NEI either. Case in point the Thaumic Lense and the Weak Infusion Stone. Both quests show as available in the quest book and I've looked up the normal recipe on their respective wikis to make sure but they aren't craftable at all. If you've changed the recipe there is no indication in the book or NEI and if you've somehow locked crafting of the Item then it hasn't unlocked when the quest says it should be available.