Yabba, Version: 1.1.2.9
Actually Additions, Version: 1.12.2-r135
Chest Transporter, Version: 1.12.2-2.8.8
Thermal Dynamics, Version: 1.12.2-2.5.1.14
RFTools, Version: 1.12-7.53
Applied Energistics 2, Version: rv5-stable-11

Pack: FTB Continuum, Version: 1.3.1

It seems when an "Auto-Breaker" breaks a "Item Barrel" it drop one in the world which is the one that has items in it but the "Auto-Breaker" has a new "Item Barrel" in its inventory, the new "Item Barrel" is empty.

A similar thing happens when you pick up a "Item Barrel" with a "Chest Transporter" which is sitting on a duct from Thermal Dynamics, The original "Item Barrel" is in "Chest Transporter" and a new "Item Barrel" is dropped on the ground.

The "Builder" from RFTools using a quarry card ( Tested with a clearing quarry card ) will do the same as the "Auto-Breaker".

The "ME Annihilation Plane" from Applied Energistics 2 also makes a new "Item Barrel"

This seems to be similar to issue #76

It only dupes the barrel, without contents? That's good at least

Yea only the barrel gets duped

After some testing it turns out I'm not doing anything wrong, because vanilla shulker boxes can be duped in the exact same way. I tested with AA Auto-Breaker and ME Annihilation Plane, and I will simply ask Chest Transporter to stop supporting it and will add easier way to drop item without taking any items