I don't know if you had a chance to go over my articles in "Attic" category - http://checkthishouse.com/category/attic
where I explain pretty much everything about attic mold. decking discoloration, etc.
Is the condition you're describing a reason to be concerned? I would do a little investigation / evaluation of the attic ventilation ports. Similar thing happened in my attic and the reason was a bunch of cottonwood trees surrounding my house. Every winter the decking and some rafters discoloration (North side) was getting darker and expanding significantly.
When I looked at the ventilation ports along the soffits they were all clogged up with cotton and dust, all it took was a powerful vacuum to remove all that contamination. One side of the soffit was easy since I have a first floor roof beneath, on the other side it took a few ladder trips to do the job.
Is it mold or not, toxic or not? You'd have to lab-test some samples to answer those questions.
In case you don't have any soffit vents, check for contamination whatever type of attic ventilation you have: upper and lower... and check my posts at the link above from more tips