Ronnie--
I think my "ovulatory dsyfunction" diagnosis was laziness on my Doctor's part. In the past year I have had 3 long cycles. (1) when I first got off the pill (2) when I hiked the Inca Trail to Machu Picchu in Peru (3) when I got a really really bad stomach virus that had me nauseus for weeks and left me 10 lbs lighter (which I gained back). During these periods, I was NOT running at all. So, no, I do not think that exercise had anything to do with my diagnosis.
I support LostGirl's supposition that it is more the amount/time/intensity of the workout combined with lack of healthy eating habits that results in amennorea.