I feel it is from using city water with chlorine added to it.
I have gotten flash rust every single time I've heated water from the tap (I live in a small city). Warm, hot, boiling...flash rust. Room temp or cooler, no flash rust.
I've read tons of threads where some say they always get flash rust with heated water, and others that say they never get flash rust with heated water. Then I read a post where someone suggested it could be from city water with additives?
So I bought a gallon of distilled water and used it the next time I needed to clean. Heated it on the stove, not boiling but very hot. Used half of it with a few drops of dish soap, then the other half just water for a rinse.
Zero flash rust for the first time (for me) ever.
I started a thread about it. Comments in the thread showed a very common theme of city water folks getting flash rust and well water folks not getting any, for the most part.
I haven't done any shooting in a while, but will continue heating distilled water and using it. I don't feel it cleans any better or faster, but I sure like how much quicker the barrel dries.
Here's a link to that thread. I'm not stating this as 100%, but I'm going to use distilled water and heat it until I see otherwise.
Warm/Hot water when cleaning and flash rust | The Muzzleloading Forum