My pond, too, for some reason, will be really clear after a rain. No clue as to why. Hmmm... wonder what it will be like after Hurricane Ike hits Saturday.
Your dark fish are probably babies from the stock in your pond. Like others said, they may well change to gold as they age. If not, they are sorta useless, IMO, because you can't see them. I just fished out a black koi whom I have had several years, and gave him to a gal with a rescue operation, because I couldn't see him. Why have a fish contributing to the poop and amonia, etc. load if you can't see him to enjoy him.
All this does not explain, however, exactly WHY I went and bought a large Black Moor goldfish just Monday. I haven't seen him ONCE!
Also, FYI, because many people don't revisit a thread once they've red it, when you have a new question or topic, it's a good idea to start a new thread with a title describing your topic. That way people will notice it, and you're more likely to get responses and answers.