Most brackish flounders can be acclimated to freshwater. I did that with my flounder when I tore down my brackish. I add one tablespoon salt per 10 gallons of water in my tank and that might make a difference to the flounder, but who knows.
Melifix is safe to use with flounders, but I don't know if it would help with your problem. It is really good at healing torn fins and small wounds but not much else. Try the meds that guppy recommends.
The best advice I can give you right now is to get rid of all the different kinds of gravel in your tank and put sand in, at least if you are serious about keeping your flounder. They really do NEED sand, small (tiny!) round gravel, or a bare bottom tank to be happy. Otherwise they get cut up, injured, and possibly infected.
a happy flounder is a flounder that can bury itself. small round gravel is fine (fine being slightly larger that sand but not much). but sand is good too
They are brackesh water fish, I just use freshwater fish salt (such a wierd concept) at about 1tbs for 5 gallons of water. If the redness is on his underside (the side without the eyes) it might be natural. I was a little concerned when i first got mine and noticed that he was reddish on the underside, but since then all of the pics I have seen of others have had the same coloration. Other than that they all have some fin wear at the front edge of their body so that might be whats causing the redness (i cant really tell from the pic). Just keep an eye on him. The waiting is usualy the hardest part.