Let me know if you ever figure it out. What you described is exactly what happens to me on every hatch. You didn't say how many didn't hatch, but if I get 50% I'm doing good! One of the main reasons I don't hatch much anymore. Especially when you spend $50+ on shipped eggs, it gets old quick. On this hatch I set 15 eggs, and ended up with 7 chicks. Only 2 were clear and/or quit. I've tried everything I know of to fix it. Dry incubating till the end, 50% humidity, and everything in between. 60% at hatch or 90% humidity at hatch.. it doesn't matter, same result every time. Tried different incubators, table tops and cabinets... same deal. Someone asked you if your eggs pipped internally... and I've had it both ways.... No pips, internal pips, external pips.... usually all on the same hatch! It sure gets frustrating.
My eggs from two different coops, only four laying so it took a few weeks, many frozen eggs in between. Didn't expect a good hatch cause of this, but didn't expect mostly viable chicks. 34 to start, pulled five clears and blood rings, and marked one that I was sure was early quiter but left in. 13 hatched so 15 that look like they should have hatched. I could deal with 15 no good at all, but this is crappy.