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Oh good, I am glad you could figure out something from my ideas.
I think you may be right about the lids causing lack of air to the eggs. Especially if they are blocking any of those air holes on the bottom. Many people do not realize the shells allow air to pass through - and if you don't have enough oxygen the chicks don't get enough to make the second pip. I have been reading a lot of threads about hatching shipped eggs and that came up in one of them. They said the oxygen is very important to the hatching chicks, and too high humidity or not enough oxygen around the eggs can cause problems. They were describing the internal pip/not external pip deaths.. so that's why I mentioned it. It came up more as a problem in the still-air incubator/hatchers too. The forced air ones had problems with shrink-wrapping...
You could try using Tupperware containers for humidity instead of the coffee lids? If you take a very small Tupperware container and cut a little slot in the top - stick a piece of sponge in the water with the end out (like a lamp wick) and fill it with water it will wick the water out slowly and keep the humidity constant without blocking the airflow..
I haven't hatched shipped eggs before, so I weighed them and marked them this time and will be watching them closely. I used to use a Hova-bator years ago but I can't use it where I live now (see signature line)... I used to hatch my own eggs, never needed any "tricks" like weighing or marking them before. I am amazed I used to get as good hatches as I did without knowing anything (usually 75% to 99%). Probably being in Santa Barbara with the ocean humidity and the wonderful weather helped too..
On my first test batch of eggs in this new cabinet I dry incubated, mostly because the first two weeks I misread the temp/humidity gauge in there as being 76% but found out it was a faulty LED screen and it was actually 16%.. I could only ever get it up to 60% for the hatching - and all the eggs hatched..
I was worried because it seemed too low at hatch, so I kept putting water in the pressboard egg cartons I was using to hatch them in every time I took out the hatched chicks, to bring the humidity up around the eggs. They started hatching on the 18th day and finished hatching on the 21st day. I think maybe the incubator was running just a touch hot... but no shrinkwrapped chicks..
for a better hatch of your next ones!