If you are losing baby chicks with in the first week, there can be several problems going on. First, you say you have hatched many babies before. Are you disinfecting this incubator after each hatch? If not, you are brooding bacteria and virus's with each hatch and this will kill babies. Incubators need to be fumigated after EACH hatch, as well as the brooders and equipment. This is a VERY important step to preventing bacterial infections in baby chicks.
Next thing that comes to mind is temperature. Too high or too low of brooder temp will kill babies. Simple as that. So you need to have a good brooding thermometer. One you get from a brooding supply place. Always keep the heat source on one side of the brooder and the food and water on the other so they not only have to leave the heat to get to the goods, but have cool places along the edges to chill out if they need to. If they are piling on each other, they are cold. If they are stretched out along the edges, they are too hot.
Next, make sure the babies know where the food and water is. Lay paper towels down and sprinkle starter feed all around the floor around the feeder so they know where it is kept. Dip everybody's beak in the water so they know where the water is kept.
Finally, if they are dying after the second week, they could be suffering from coccidiosis outbreaks. A parasite that overwhelms the babies from the poop and causes lesions in the intestinal tract. Babies will have bloody dark runny poop, sit fluffed up in the corners, not eat or drink. This hits babies between the ages of 2 and 4 weeks. If you suspect cocci, and as long as you are not feeding medicated starter feed, get some Corid from the feed store and use this in the water for 5 days. Keep the brooder VERY clean and dry and this will help stop the deaths.
Sorry about your babies. I hope you can get this solved soon.