According to the creator of Ex Nihilo the item duct issue is:
"Basically, TE looks for inventory slots on machines that it is connected to. The crucible has one input item slot for the itemduct to look at. Minecraft item slots can hold a stack of items, but the crucible can only hold one item at a time. When the crucible can take another piece of cobblestone, I open that slot up to be filled. The itemduct takes a STACK of cobblestone and tries to put the whole stack into the crucible at once. The crucible takes the one item it needs, closes the inventory slot and gives the rest back to the itemduct. If the itemduct can't get rid of the extra somewhere, it just bounces around in there.
The crucible is not lying to the itemduct or anything. In fact, the only way that I 'could' solve this issue is by lying to the itemduct and saying "I have 63 cobble, please just send one" even though my inventory is empty.
EDIT: I also want to be clear about why I don't want to fix that. Most people haven't tried this, but the crucible can melt smooth stone, gravel, netherrack and obsidian in addition to cobble. If I lied to the itemducts and said that I have 63 cobble, piping systems would assume that they couldn't put in anything except cobble.
If you want to eliminate this problem in-game, just put a hopper on top of your crucible and run the itemduct to it."
Its a cross mod issue not an item duct issue.
Also a Jabba barrel with a hopper upgrade works great!