In NuclearCraft (both normal and Overhauled), there is a recipe:
250mB Oxygen + 500mB Hydrogen -> 250mB Water
registered by NC to the GTCE Chemical Reactor.

This recipe overlaps with another recipe added by GTCE:
4B Hydrogen + 1B Oxygen + 1 Carbon (circuit 3) -> 1B Methanol.

The Water recipe will always be chosen, and Methanol is currently uncraftable using this recipe when NC is included with GTCE. If a Integrated circuit of anything other than a 3 were included, or if this recipe were removed, then the problem would be addressed.

NC (at least in the overhaul edition) adds a recipe to make methanol (250 mB) by reacting carbon monoxide (250 mB) and hydrogen (500 mB) together. Does that recipe still work for you?

@DStrand1 Fixed by generalising search for recipe conflicts :)