As the title states it will only let one item go into the output slot. If I put 5 logs in the top and fuel in the bottom, it will only make 1 charcoal and then stop. I have to take that 1 charcoal out before it starts making another one. It's not an issue with stacksize because it stacks fine in my inventory. I have tested it and works properly with only FastFurnace installed.

Mod list: https://paste.dimdev.org/itedarucej.md

FastFurnace Version: 1.12.2 1.2.1
Forge Version: 14.23.5.2772

Experimented and it happens with FastFurnace and CustomNPCs installed.
Log: https://paste.dimdev.org/uvovokuceh.md

(versions of other 2 are still the same) CustomNPC Version: (26Aug18)

This is likely on their end, and since CNPC is closed source, it's not something that I can fix or even look into.

Someone asked Noppes and he said he couldn't fix it on his side.

There's a reddit thread here that looks like they may have found the source of the issue.

That makes the issue entirely on their end. That significantly breaks many comparison methods. Nobody should be randomly attatching NBT information to every itemstack.

Shadows added a config option Strict Matching in 79a25e3/v1.3.1 which you can set to false as a workaround for this issue.