I've actually asked about this before, but all my lighter shell shoes develop dark gray or black streaks along the creases. I have tried using damp cloth, extensive brushing, and Saphir Renovateur, but nothing lifts out the grime. I have chalked it up to Los Angeles air pollution, combined with miles of outdoor walking to and from work. So far, this theory is supported by the fact that shoes I've acquired since starting a new job to which I commute by car exhibit none of this black streaking.
My whiskey chukkas have a bit of the same issue. Living and walking in NYC attracks the NYC "grime" sometimes (and I walk a lot in my Aldens). It is what it is. I can brush and shine them and they will look good and have the regular cordovan glow, I still will have some marks.