OH I know what it is. I don't have a null check when producing outputs for the first input slot, because that was mandatory to have filled. When introducing the permeability of crytsalliser recipes, that might have been changed. Whoops. Then it'd make sense.
Nah not that very issue, but it still was made possible due to the permutation changes. Fixed in my dev environment but unfortunately I cannot fix it on 1.6.4 anymore.
As a temporary fix, either disable the Crystalliser or make sure you only use the recipe exactly in the order that NEI tells you.
I did disable it and the server survived the night. Thanks for the foresight and the config option 
