I can't say I know how to fix this without looking at it.
I know there were several key changes to the system - likely when the other bod systems were expanded. This past summer the S7BodfillerX project was completed and can fill most bods. It definitely works for all tailor, smith, inscription. I believe it works well for most, if not all, of the current alchemy, fletching and carpentry. Cooking it can fill, but doesn't make sub components and there are a lot of those in cooking.