I have never used ATS before but from what I have read, you need to seed your ATS with algae.
IMHO, if you don't seed the ATS, the ATS will be populated with whatever micro-organisms / alga that is available in your tank. From the looks of it, not only diatoms but cyano bacteria has colonizes your ATS.
I am not sure whether this will be temporary, it has been documented that Cyano and Diatoms are the first to colonize bare rocks in nature.
Just my thoughts, maybe reefer will more experience with ATS can advise.
Source:
http://www.chucksaddiction.com/The%20Natural%20Reef%20Aquarium.html
http://www.who.int/water_sanitation_health/resourcesquality/toxcyanchap2.pdf
http://plankt.oxfordjournals.org/content/19/12/1793.full.pdf