it's probably the primer color, of two different quality. the color variation can be due to a sort of rust protection primer. or a primer that is designed to withstand heat or blast where they expect it to hit most... ho know, but it's a primer of a sort.
for those ho doesn't know what primer are:
http://en.wikipedia.org/wiki/Primer_(paint)
but if I think a bit, it can be that not the entire superstructure was finish painted, so some of the superstructure got the primer, rest was unprotected metal with a bit rust on it... so the orange could be an marking of that area that wasn't primed yet.