Billyruffn - the taste is coming from the tank, not the water; I had the same taste after I filled the forward tanks at the dock so the source isn't the watermaker.
I sent an e-mail to the manufacturer and am awaiting further information from them.
I'm unsure from the above if you've taste-tested the water coming directly from the unit. If not, you could be putting bad water in the tanks.
There has to be a source of the dark water coming from the brine discharge -- the last thing before the exhaust seacock is the membrane. My guess is it's contamination on the salty side of the membrane, although it could be in the filters before the membrane and pumps. You'll just have to trace the source of the contamination starting at either end of the process. Have you checked the filters? Color of water coming from the filters?