To comment correctly on your hone, then photos as you know would greatly help,,,with that said, there are dark spots on my Zulu also, but they are small & I not even sure were are talking about the same type of spots. But a good lapping of mine negates any problem with the spots.
I also use a DMT 325 & 1200 on my Zulu, lapping under running water, this makes my lapping of the Zulu quite easy compared to other stones I have.