roof stains

Can anyone tell me what the stains that I see on mainly light colored rooves are caused by? The stains are triangle shaped. We see them all over here in new jersey. I've been told they are from shiners( exposed nails or nails left on the roof), caused by trees( but there are often no trees in the area), mildew or mold( but why the triangle shape?). I've opened bundles of shingles, usually plastic wrapped, that stunk like wet laundry left laying around. I believe the stains are caused by a manufacturing/shipping problem(ie;frozen shingles). Could they be from installing the shingles on a real hot day, when the roofers shoes are breaking through the surface of the shingles? I've been asking the questionfor a few years now. The suppliers say they don't know, but they offer a more expensive shingle that is sealed/treated that supposedly doesn't stain. Hmmm. Any ideas???/answers...

 

could you get a picture of the stains on the internet?
maybe i could help if i seen them.

 

Boy, what a dope! Here I bought a didital camera last Christmas. Excellent Idea! Thankyou, thankyou>Will do ASAP.