While a huge tank has some advantages (stable water quality), it has the disadvantage that the food is spread out over a large area. Daphnia tend to congregate in certain areas of the tank (usually the most brightly-lit spots), which makes for an uneven distribution of food. Hatchlings are not too smart about moving toward where the food is. Thus my speculation is that the ones that died simply weren't finding enough food in their immediate vicinity. This would also explain why some of them are monster-big.
I would suggest adding more daphnia and stirring the daphnia around a couple of times every day. And if you have some other kind of food you could add (such as BBS or whiteworms), this would also help.