Based on her diet, it is almost certainly a nutrition problem. Seed mixes are a bad base diet for almost all birds, definitely conures. Papaya, coconut and apple are good but she needs many, many more fresh vegetables in her diet, and a much wider variety. Carrots, bell peppers, spinach, kale, lettuce leaves, hot peppers, zuchini, yams, squashes, beans and pulses, sprouts, corn, peas...the list goes on and on. Pretty much anything but onions and avocados!
Seed mix is way too fatty for these birds. You should try to wean her from seeds and switch her to a healthy pellet diet. Harrison's, zupreem and roudybush are some of the recommended pellet brands that members here use.
She can also have small amounts of (fresh, raw, unsalted and unflavored) nuts and seeds (although peanuts are often avoided). Some particularly healthy options are flax, chia (but make sure it's soaked first), sesame, almonds, pecans, walnuts, pumpkin seeds, and the occasional cashew, sunflower seed and pistachio.
As for fruits- you're on the right track! Any fruit but particularly those low in sugar- papaya is a good option, but also berries. Apples are high in calcium so they make a great treat, as do pears, mango, cherries, nectarines, plums...make sure everything is peeled and washes and like I said, don't over feed sugary fruits. Vegetables are more important.
Your newest little one, at three months, is probably not long weaned and I would guess has only been with you a few weeks? Her feathers will start to blacken too if you leave her on the same diet apple has been on!
Hope this helps.
