Honestly I was expecting poor water as this is the most common problem with mollies.
They need good water quality or the commonly suffer these sorts of problems.
Your doing everything right so you should not worry if there anything else you could do to help.
I would guess that something came in with the new fish or he's had a prolonged problem but was able to cope with it. When you added the new fish it would of caused a mini ammonia spike which may of caused the problems to show.
Best i can offer would be doing extra water changes as fresh water dose help, and adding some melifix once a week.