I'm not sure if this is the place to post this. I did a quick google search and found no information on this. 

ShapedRecipe.setIngredient(char key, MaterialData ingredient)

does not implement metadata as it would so suggest

Tracing the API, it uses deprecated methods that converts MaterialData into a Material object and a raw int. the int never actually gets used in the end, so all your left with is a Material object, thus losing any metadata the ingredient had initially.

This makes using certain items impossible. For example coding a recipe that requires an Enchanted book, will allow using any enchanted book instead of the specific one that was originally set.