I placed down an alloy furnace and put gold dust and iron dust, both from Metallurgy 4, in the alloy furnace and it produced gold without using either the gold or the iron dust. Also, after breaking and replacing the alloy furnace, it continues to create gold ingots without any ingredients (Still uses the fuel).

Using Bluepower 1.7.10-0.1.747 + Metallurgy 1.7.10-4.0.4.43

This sounds like a mod has added a recipe that uses gold ingots without an output item. We'll be adding in a check to make sure that recycling recipes are valid.