Copper, yikes! I hope you don't plan on ever having invertibrates in your tank. While I am probably one of the few supporters of copper use left (as last ditch measures and at low theraputic levels) there are definatly other medications out there that can combat velvet without copper. Now that you have used copper, it is pretty much in your system for good, absorbed into the rocks, substrate, and equipment.
I'm not familar with velvet looking like brown algae on fish. Velvet appears as if the fish are covered with minute mica "gold-dust" speckles and is usually all over the body, not just restricted to certain places such as throat and fins.
I know on some gourmis, the males may go through a color change around that region as they reach sexual maturity and are looking for a mate. I'm not sure if this is true for paradise fish, but look it up.
Algae-like growths usually signal bacterial/fungal infections. Maracide is a pretty good medication for those.
~~Colesea