Dave, if you have tried 10 percent of the advice in this thread you should not be having a re-occurrence of rust in your bore. As a minimum, if you do the hot water cleaning routine, followed by patching the bore dry and then using an oily patch after drying, you will not have a rusty bore. What does an oily patch look like after you have put it thru the bore 10-12 times? Maybe you could post a pic of an oily patch after swabbing the bore. About the only thing that hasn't been suggested here is to use Kroil, a fine penetrating oil, which will ooze into every crack in the bore and dislodge rust. It is so viscous that it will even get underneath metal jacket fouling and help to dislodge it. Maybe you could also post a close-up pic of the muzzle. Traces of copper jacket fouling in the bore can be mistaken for rust.
I'm not trying to tell you how to suck eggs here(maybe a bit though), but I and others are intrigued by this unique sounding problem.