Freshwater Disease Charts
Myxobacteriosis
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Symptoms: Symptoms may include black patches on the body and fins. The body may become bloated or swollen in some areas.[/FONT]
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Treatment: As far as I know, there is only one medication designed specifically for myxobacteriosis--Phenocide by Aquatronics.[/FONT]
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Information: This infection is rather uncommon but fairly easy to treat. Its probability is intensified by overcrowding and poor water quality with high levels of ammonia and / or nitrites.[/FONT]
I guess that since the blackness has started to go away it may have been Melanophore migration due to something stressing them out. Maybe the water PH rising suddenly contributed when other factors were already stressing them. Melanophore migration can also show up in conjunction with a parasite infection. Did you mentioned that your goldfish weren't pooping normally at some stage? If so you could possibly have a growing infestation of worms in your fish. Does it ever look like they have white strings trailing instead of poop? I would probably think that not all goldfish would show the same signs when stressed so it may lean towards Myxobacteriosis because they all did show the symptoms.
I couldn't say if ether of these issues are what has been giving you a sick tank but the symptoms for both match and might be something to go on.