You might crack your unhatched eggs and compare them to what they say in these links. Something might jump out at you as to the cause. You have observed the whole process and I have not.
Mississippi State Incubation Troubleshooting
http://www.poultry.msstate.edu/extension/pdf/troubleshooting_incubation.pdf
Florida Incubation Troubleshooting
http://edis.ifas.ufl.edu/aa204
I'm not sure if you have fans in there or not. I think I see a couple, but not sure. I don't think this is your problem since they are developing in the different trays, but in a still air, the temperature varies throughout the incubator since hot air rises.
I suspect humidity could be your problem. You need higher humidity during thatch than during incubation. I suggest you pay close attention to the humidity signs in those links.
Another possibility, also humidity related, is do you open the incubator during lockdown to turn eggs in the top trays. You can release humidity doing that and sometimes cause shrink-wrapping the chicks that have pipped.
Another thing. How is your ventilation? Chicks need oxygen when developing but especially during hatching. Arethey getting enough oxygen?
There are many things that could cause a problem. Hope those links help.