I've been trying, on and off, to reliably reproduce and investigate this Thaumcraft bug report I made a while ago: Azanor/thaumcraft-beta#1371

After a long and confusing Odyssey, I have finally narrowed it down, and submitted the following bug report to CraftTweaker: CraftTweaker/CraftTweaker#652

However, since Baubles is required to reproduce it on my end, I'm also opening a report here, so that you can look into it.

After review by a CraftTweaker dev, it might actually be intended behavior... except that the intended behavior disappears if Baubles is not loaded? That ought to be one of the strangest interactions ever.

Summary after finding the root cause:

Minecraft's furnace code takes the first recipe that produces a given result that it can find, and uses that recipe's parameters for all operations that produce the same result. In this example, it will use the parameters of the first recipe that returns iron ingots for all smelting operations that yield iron ingots.

However, the list of recipes does not preserve order. Therefore you cannot predict which recipe will be found first, even from one client to the next. Additionally, everytime you add a mod that adds at least one furnace recipe, it essentially reshuffles the list, and may cause different recipes to be found first.

Bottomline: this cannot really be fxed on your end, so I'm closing this. Hopefully it at least helps you diagnose related issues in the future.