I can tell you from recent first hand experience that AE2 will only use the 1st valid recipe it sees. In my case I have magic crops that can produce glowstone. Well before I set that up I had a pulverizer recipe to craft glowstone from glowstone blocks. I wanted to craft something that used a large amount of glowstone and it wouldn't do it and kept insisting it didn't have enough glowstone blocks. Removed the pulverizer recipe and everything worked great.