This problem only occurs in Slot 2 (the output slot).  Every other slot shift-clicks just fine, but slot 2 likes to leave a size-zero stack behind, for no apparent reason.  I've double checked my code against other Container classes and nothing seems out of place.

 

@Override
public ItemStack transferStackInSlot(EntityPlayer player, int slotNum) {
        ItemStack itemstack = null;
        Slot slot = (Slot)this.inventorySlots.get(slotNum);

        if (slot != null && slot.getHasStack()) {
            ItemStack itemstack1 = slot.getStack();
            itemstack = itemstack1.copy();

            if (slotNum > 2) {
                if (RecipeManager.getSiftResult(itemstack1, false) != null) {
                    if (!this.mergeItemStack(itemstack1, 0, 1, false)) {
                        return null;
                    }
                }
                else if (slotNum >= 3 && slotNum < 30) {
                    if (!this.mergeItemStack(itemstack1, 30, 39, false)) {
                        return null;
                    }
                }
                else if (slotNum >= 30 && slotNum < 39 && !this.mergeItemStack(itemstack1, 3, 30, false)) {
                    return null;
                }
            }
            else if (!this.mergeItemStack(itemstack1, 3, 39, false)) {
                return null;
            }

            if (itemstack1.stackSize == 0) {
                slot.putStack((ItemStack)null);
            }
            else {
                slot.onSlotChanged();
            }

            if (itemstack1.stackSize == itemstack.stackSize) {
                return null;
            }

            slot.onPickupFromSlot(player, itemstack1);
        }

        return itemstack;
    }

I can't really tell you why, because I didn't ever tryied myself in transferStackInSlot, but if the stack is correctly moved, you could try it with a

//add in here any Method which checks for a working Recipe or something like that
if(slots[2] != null && !doesRecipesWork()){
slots[2] = null;
}

 

Ha, turns out it was my own stupid fault in the TileEntity class:

 

@Override
public void setInventorySlotContents(int slot, ItemStack stack) {
	if(slot == 2) {
		return;
	}

 

Amazing what a night's sleep and fresh eyes will find.

What the hell did you think there

 

No idea!

That was written weeks ago, my best-guess is I was thinking "this slot is output, shouldn't be putting anything into it!"

And I had to change the TransferInSlot method last night because it was still a duplicate of the furnace (it was checking furnace recipes for slot validity).  Lots of little stuff that at first blush looks to be working right, but isn't, heh.