I'm not sure if what you have going on is the same thing or not, but on a few jobs of mine I had some small black stains at the peak also. After looking into a little more I realized that these stains were only on roofs with the painted aluminum ridge vent, and that the stains were located at the seams or weep holes of the ridge vent itself. My guess is, that these stains were caused by the removal of the oxidized paint over time, that had drained from the ridge vent channel and had left streaks that look identical to GM. If this in fact is the case, then what will remove the paint from the shingles?