Years ago, I had a green coneflower. It always bloomed green. Never had any other issues. I posted about it on gardenweb, and contacted Tony Avent of Plant Delights. He said it was a case of Aster Yellows disease. Well, a few years later, hybridizers started coming out with all these new colors of echinacea, and one of them was green like my plant!
Don't know if yours has aster yellows or not. What is the name of that echinacea? Is it supposed to have petals on top? Like Doppelganger?