Barrel break-in must be done properly on every new barrel... (Custom and factory) if you want it to shoot as acurrately as possible.
Each new barrel has a very rough throat due to the chambering reamer. Even hand-polished custom barrels cannot smooth out the throat. This can only be done by shooting a bullet through it. Each time a bullet passes through it the throat becomes smoother.
Imagine the throat is like coarse sand paper after the chamber is reamed. When you shoot your first bullet, the sandpaper rips your bullet apart and due to the massive temperatures and pressures associated with the discharge. The copper in the bullet is turned to plasma and is deposited all the way down your barrel. You now have a new copper-lined barrel! The problem with this is that it creates a platform for more buildup and soon your bore is full of carbon and copper and its a booger to ever get that stuff out of there. This absolutely destroys your acurracy.
So, the process is to shoot one and clean. Notice the large amount of fouling present. Shoot another and clean. There will be less fouling because the throat is now a little smoother and doesnt rip as much of your bullet apart. Repeat this process several times while increasing the number of shots fired inbetween cleanings as evidenced by the diminishing amount of fouling present. Soon you should be able to shoot several times and experience little fouling.
The X-factor is the quality of the barrel itself. Most (if not all) factory barrels have a significant amount of tooling marks that were made during the rifling process. We look through these with a bore scope and it looks like a bulldozer left tracks down the inside of the barrel. These "tooling marks" in a "rough bore" will continue to serve as a place for the fouling to be deposited and build up for the life of your barrel. Some factory barrels actually have 1-2" spaces where no rifling exists at all and a higher-than-expected number of the barrels are found to actually be warped as we spin them off!
Conversely, the inside of a custom barrel has a mirror-finish and subsequently has nothing for the fouling to stick to. Thats why you can shoot all day with a custom barrel and its clean after only wiping with a few patches. Most shooters with these barrels find that they rarely need to clean. But again, even these barrels need to be "broken in" in the beginning because the throat is always rough after the barrel is chambered.
Here is the best explanation I have seen: