I've seen this on BOTH Rams that i've had... First was the 2001 and again on my 2005. I think the "rail dust" on the paint is a load of crap. My $0.02 says its the brake/rotor dust that gets stuck to the paint, then rusts... Brake pads are all metallic now... you'll only see this on white or other "light" colors.
This past winter was the absolute worst on my truck... 262 inches of snow here, and i pulled it into the relatively warm garage every night - for it to melt off and rust. I've got rust showing on the bottom and inside of my tailgate with only 55K miles.
Clean all you want... it will be back - even this summer. Been there, done that.