By late stage you mean the last few days, right? Chicks fully developed?
Did you have a look inside the failed eggs afterwards and if so, what did it look like? Egg yolk absorbed?
You can open the incubator every day without a problem (the hen leaves her nest daily too) except avoid opening it for the last 3 days and definitely don't do it when any eggs have pipped.
If you did that then another cause could be that the chicks grew too fast and had no space to turn to get in the right position for hatching (assuming ducks need to do that the way chickens do), though if they were at the right weight for their breed then that wouldn't explain it either

I've only done the weighing system once, all the other hatches I've done by humidity measurements alone (and both fertility and hatching rate of our own birds is 90-95%).
What a shame about your hatch
