I have the same stains around both A/C's. I believe the staining of the EPDM roof is caused by traces of copper oxide that leach into the the condensate from the evaporator copper tubing sweating. It is probably more prevalent where the A/C's run more often in high humidity, due to more condensate runoff than in other areas.
We've been full-time in Florida for a year and a half, so the A/C's have a lot of run-time from April through November, and there is a lot of condensate runoff due to the high humidity.
Copper ore and copper oxide are green in their natural appearance. When you see old copper pipe, wire, roof caps, etc. the take on a dark patina and eventually green oxidation.
That's my guess anyway. Cheers.