I've dipped black Cerakote-C(high temp), black anodized aluminum, and melonited black stuff....they are all tainted color wise...but they come clean. I'll get the stuff recoated if it gets too bad.
I use 50/50 Simple Green mixed with RO water. I do use the heat setting on my ultrasonic as well and my stuff is fairly hot when it comes out. That could be a factor.