What is your incubator temp? You said it's constant but what is it? Also, are you using just one or two thermometers to check it, maybe one is off? Too low of a temp can cause dead but outwardly perfect full-term babies.

Otherwise it may have just been that particular pairing that was the problem. I run my eggs the same as you, sealed plastic container w/ the Glad Press n Seal to maintain humidity at 99% or higher, and open the lids to permit air exchange briefly once a day for the last few weeks.