I've got a few thoughts, as well as a few questions. First, I've shot the Judge using both .45LC and .410 loads. I had great results from both. The .45LC was absolutely accurate enough to serve well as a self defense revolver. This isn't a pistol you buy for match accuracy. It is a self defense gun, period. They are developing several new .410 loads specifically for this revolver, you should look into them. The .410 loads I fired from 10 and 15 feet were quite effective. At 5 feet, that load will probably tear someone's face clean off. Used as a defense gun for potential car jackers, the .410 load would be devastating.
Without seeing your barrel I really can't do much more than guess what's happening (if anything). If you have been firing alot of .410 loads, you could have leading (lead fouling) or more likely it could be plastic fouling from the wads. It's particularly hard to remove because it's just about impervious to solvents. One product that I swear by is "Eezox", it works. You should also work it with a brass brush. This barrel is manufactured far differently than your standard barrel. It's designed for two purposes, to fire centerfire handgun rounds, like the .45LC and .410 shotgun rounds. The rifling is cut very shallow to allow proper passage of the shotgun pellets but still high enough to impart adequate spin for the bullets used. So you have to realize that this barrel isn't going to look or behave like anything you've used before. It has been genetically engineered!! Here is a website with a picture I want you to look at
http://www.notpurfect.com/main/taur410.html . Look at the third picture, the one looking down the barrel. Do you see those areas that look smeared or smudged? Is that what you're seeing? If so, it is entirely normal.
If you aren't having any trouble with it and have had it inspected by a qualified gunsmith, I wouldn't be concerned about it. See if the smudges you're seeing might be a shadow from the differences in machining or plastic residue from the wads. This is a very tough revolver and if you're not having a problem with performance, I recommend you just enjoy it!!