It is not currently possible to auto-craft the Herculean or Gargantuan flux storage devices in Refined Storage (have not tried AE2 recently but it didn't work last time I did). It seems the crafting recipe for them yields a block with an NBT tag immediately on it, which is throwing off the auto-crafting calculation in RS. I'm not sure if this could be fixed on Refined Storage's end or not, but it could be fixed on Flux Networks' end by only adding the NBT tag onto the item once it has been placed in the world once.