Thats the Manager. The Manager emits Redstone, what is disabling the Matterfabricator. Eloraam should make her Manager not outputting Redstone in the Direction it is facing. Same with Regulator.
Or add a small button in matterfab GUI to revert its redstone behavior, if possible. If not i suggest using a chest + GT translocator to move scrap inside the matterfab.
So do I. (Failed at quoting :p). But ... the Idea of replacing the Sulfur by Sulfuric Acid was a good one. Just make it obtainable by some other means. (Or make it create 3 batterys ^^)
Got a question, factorization sulfuric acid can be used for that?