They really should tell you about the staining when using API Fungus Cure. All they say is, Note: This medication will cause a slight discoloration of water which can be removed with activated carbon. I've used the API Furan 2 before and it made the water yellow but didn't stain anything and cleared right up by adding activated carbon to my filter. I was real leery when I used the Seachem ParaGuard so I called Seachem and asked about staining and they told me no it will not permanently stain.
Just like to give an update. My yellow Cichlid with the white pectoral patches on fins. Well for the past week his white patches went from white to grey and now black. Looking closely the patches are actually gone and I’m guessing the black is basically scar tissue or dead cells on the fins. Not sure what medication worked or if it was just time. Either way a couple more weeks in the QT tank and he might be able to join the community. However, I just noticed two of my other cichlids have fungus growing on mouth and fins. I don’t understand, I do water changes sometimes twice weekly, my parameters are perfect, not overfeed. I just don’t understand how these issues keep popping up.
Have you added any new fish to the aquarium lately? Are any of the fish being aggressive to other fish? I went through something similar a few months back and finally got rid of the fungus or whatever it was by using Seachem ParaGuard in the aquarium and mixing Seachem KanaPlex in the food.