A couple things first:

Did all the eggs candle as good?

What did you use for a mixture of water and substrate beneath the light diffuser?

Are you covering the egg box with press and seal?

I have not used substrateless but have read that in doing so you can be way over on the amount of water as the eggs will not be in contact with the substrate anyways. Try adding water and press and seal if you are not using it already.