I want to lean on the side of caution and say the black flecks are mold. Your older birds may be less effected because they are less fragile.I am not ruling out toxic fumes yet, but if that was it, they were in there for two days and we covered the whole thing with a towel at first to protect against drafts. If it was gases from the bulb or vaporized chemicals wouldn't that have been when the problem occured, not with it wide open? I washed out the aquarium with just dawn and water, and rinsed and dried it well, I did not use bleach. And before I was worried about the bulb they were already in the new brooder with the same bulb but I haven't lost any more chicks.
What did change is the Aquarium, paper towels and the feed.
I checked the feed, It does not look moldy. It doesn't smell really fresh though, but I may be over- smelling. There are black flecks on the bag itself, could the smaller particles trapped in the creases and weaving of the bag mold? Can the fungus be present but not overtly detectable?
I am feeling a bit better though, I thought it was Mareks at first, before I thought about it and realized there is an incubation period. I bought some birds at a swap this fall and they died as soon as it got cold and I have been worried that I may have brought something in to my flock. They were housed seperately, but, you never know. I will NEVER buy a bird again, watching those beautiful little chicks die was so horrible and I was powerless to stop it. I have not had the experience of losing birds in a group like that, it is so scary!
Changing the food and the heat lamp would be the safest.
It really doesn't seem like Mareks
If there is something in your flock (like they are unaffected but your new baby birds are), a simple alcohol based hand sanitizer would keep it from spreading. All you would have to do is use Purell before and after handling. Use roughly a dime to quarter amount and rub thoroughly till dry. Make sure you get all over your hands, wrist and in between the fingers.
They will come into contact eventually but you may want that when they are older. All flocks carry their own special disease pool variety.