Maybe you should under dose the malachite green. Most malachite green solution contains copper. Why don't you use methylene blue- under dose about 50% from the recommended dosage. Anyway, I am not sure what is wrong with your case.

This is what i usually do - I add methylene blue and a lot of air stone(air pump) to the tank. No water changes until the fries are about 1.5 to 2cm. (probably takes about 2 weeks) - once the fries reaches that length, max. of 10% water change daily. I usually feed them with powdered fry food, crushed flake food and Daphain until they are about 1 in. After that, I tend to add blood worm into the mix.

BTW, what kind of cichlids are you breeding?