It sure feels like they are under the paint. There is a little bump or bubble where they are right now, but it doesn't feel like a break in the paint coat.
That is very interesting regarding the rail dust. Would've this been something that I would have noticed when I bought the car, or takes place over the course of a winter? Will I see this re-appear consistantly in the future?
I've taken a picture of a trouble area, maybe you could take a look and see if this resembles what you have seen in the past.
http://swart.ws/PaintAcne.jpg
The black spots are little tar things I haven't scrubbed off yet. I got pretty discouraged after not being able to remove the rust spots by scrubbing and quit detailing the truck early.