How long did you do the f/w dip for? If it was more than 3 minutes and you didn't see any tiny "worms" fall off or out of him (especially around the gills) then you can probably rule out Flukes.
It's good you have him QT'd. This way you can figure out what's wrong with him and begin treatment without affecting the rest of your tank.
"Popeye" is more of a condition than an actual disease. His eye is "popeyed" either due to injury or infection. If it's injury, you can possibly ease the swelling by adding Epsom salt (1 tablespoon per 5 gallons of water) to the QT. If this doesn't help after a few days, assume it's an infection and use the Maracyn.
In the meantime watch him closely for additional symptoms: flashing, scratching, head twitching, stringy white poo, white "sprinkles" all over his body. You need more symptoms to make a proper diagnosis.