Could possibly be bacterial infection, common bacterial issues is navel infections.  Chicks are alive one moment,  dead the next.
Make sure you are thoroughly cleaning every surface in your incubator,  any sponges or flooring used inside the machine. Brooders too, disinfecting between each batch of babies. I'm not sure what else might be getting them, I doubt it's viral. 
Also...always wash your hands after handling your adult birds before touching babies, the adults can harbor things to kill your chicks.