It sounds like you have your gray dump valves open while you are dumping the black tank?
Suggesting you leave the gray tanks drain as they fill. I would expect the black tank to empty into the gray tanks if the the gray tank valves are open. Not a good idea in my opinion. I would close the gray valves before dumping the black tank, but that's just me.
As far as your issue with the fluid left in the system after dumping you could add food coloring to one of the tanks to see which is the culprit. A tablespoon full should do it.