This is more of an early-game problem, but right-clicking items from a stack in your active cursor in order to insert them one-by-one into the Extra Utilities 2 Furnace will make one of that item appear for processing, and then every successive item you right-click into the Furnace while that first item is there will disappear. It's not a problem if you just split the stack in your inventory and then left-click them into the furnace, but this is a bug that I've noticed. I suppose it highly encourages you to switch to the Redstone Furnace, but it's still an issue for those in early-game pre-scandium/indium.

I noticed a similar issue with the "Culinary Generator" of the same mod. If I add more items of a fuel that already sits in the processing slot, they will vanish if I place them with my cursor, but will properly add if I shift-click them from my inventory.