Little what are you crafting? It might not work for crafting if the number of inventory spaces stays the same after the success of a synthesis.
For a random example, I'll use Distilled Water that was created using a lightning crystal and a Tahrongi Cactus. Tahrongi isn't stackable, so you will always lose 1 space in the synthesis, so it'll be -1. But if you get a distilled water in return, that's +1. Which equals 0, and if it equals 0 then the auto-sort doesn't kick in.