i have had that problem before, i came to the conclusion that it can be caused by a combination of certain powders and certain oils and what I had was a stain rather than rust.
+1
i know what flash rust is and thats not it. The bores of my guns are not cleaned with hot water or any water at all. Some of my muzzleloaders go for months without being fired. The brown discoloration is on the patch when the bore is swabbed prior to loading.