Cleaning Issues... HELP!

I don’t have a borescope and have since moved on to a smokeless muzzleloader. The spots in question were where the barrel is recessed a bit for easier loading. I never seen any pits. But it shouldn’t cause discoloration either. At least not in under a 24 hour period
I shoot mostly smokeless now as well and have seen small spots in the bores of my SMLs (using a borescope). I don’t get too concerned.

I’ve left bh209 fouled barrels go for 6 mo to a year without cleaning. No pitting/corrosion.
 
I have a Traditions Nitro Vortek that I bought on DNR auction. Thing was almost rusted/gunked shut. I scrubbed the every love $h!t out of it and got it 99% back to new. However there is a little putting in the bore and my patches come out similar to yours. I figure it is a little bit of rusting. I get it as clean as possible and call it good. Gun shoots incredible...No idea what the moron that got it taken away by the DNR shot through it but I've shot 777 Pellets, BH209 and currently use 777 FFFG through it. Cleaning patches come out the same no matter what powder and I just use clear grease on the threads but that is done after any barrel cleaning.
 
Thanks for all the responses. I have more supplies incoming that should be here Wednesday.

Plan is to try an oil based solvent. Whatever it is, it seems like the Thor solvent mixes with it (but isn't attracted by it) and then the dry patches pick up whatever gunk is in there.
 
I feel like an idiot.

PSA: clean your cleaning jags. Whatever the mystery brown stuff was, it seems to now have gone away once I cleaned/scrubbed my jag. And yes, there was brown stuff coming off of said jag.

I think I put the jag away damp last time and it developed a patina. Now that it's clean, I don't seem to have mystery brown dry patches.
 
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