When you say that you've hatched eggs before and had great results, were the eggs also from young ducks (<a year old)? I've found that, sometimes, young layers' eggs are more prone to hatching issues than mature layers.
Also, have you already verified the accuracy of temperature and humidity readings with a separate thermometer and hygrometer?
There are a number of possible reasons for what you're experiencing, including lack of genetic diversity - how closely are the parent stock related? What happened with the two ducklings that died during hatch?
I know how disappointing it is to have what seems like a promising hatch not work out that way. Best of luck in tracking down the source of the issue(s)!