Sometimes when incubating duck eggs at the recommended temperature and humidity, they appear to develop correctly but die in the shell before pipping. This seems to be a common problem that people have, even though they have a modern incubator, often with automatic temperature and humidity control.
There are a number of reasons why a duckling may develop inside the shell but never hatch. If you refer to the incubation troubleshooting guide, there is just about everything listed from the wrong temperature, lack of turning, insufficient ventilation and even disease in the parent flock, however with a small amount of detective work, you can hopefully rule some of these possible problems out. For example - is the temperature right? Checking the temperature with a known 'good' thermometer soon rules this out and checking the parent stock over for good health soon reduces the chances of disease. I have found two other problems though that seems to affect hatches the most.
The first problem is that as breeders improve their stock, they practice fairly close in-breeding and line breeding. This is a good way to get the desired looks and characteristics in the offspring and with careful selection and a closed flock, they can get fantastic results however after a number of years of doing this, eggs can become harder and harder to hatch and the chicks / ducklings get weaker and weaker. This seems to happen the most with chickens but it is not uncommon for this to occur with waterfowl too.
To get the best hatchability (although be careful, this is not necessarily the looks or characteristics of the parent birds - see Breeding Pure Breeds of Chickens for more information) you need the parent stock as unrelated as possible. If you suspect the parent stock has been closely bred for a number of years, introducing some new blood should give you some better results. If you are buying hatching eggs, on Ebay for example, try to establish whether other people are successfully hatching eggs, (not just having fertile eggs) comments like "4 lovely ducklings, thank you!" are the comments you are hoping to see as well as pictures of ducklings the breeder has hatched themselves. Ideally, go to a reputable breeder, such as a breeder listed in the British Waterfowl Association Breeders Directory (available when you join) or another club or organisation. Remember it is very easy for anyone to advertise fertile eggs on Ebay! Most specialist breeders will not sell eggs but will hatch eggs themselves and then make stock available in the autumn after they have selected them and taken what they want for next years breeding pen.
The second problem is one that is more difficult to eliminate from the potential list of problems and that is whether you are maintaining the correct humidity. A separate article - What humidity should I use to hatch my duck eggs? goes into a little more detail on the 'right' humidity for your hatching eggs. If you read this then you should hopefully be able to look at the size of the air sack, or use the weight loss method to ensure your eggs are subjected to the right humidity levels over the incubation process and see an improved hatch rate.
The size of the air sack at the wide end of the duck egg (in the top of our picture) on a given day of incubation is the best indication of how much weight the egg has lost and with experience and the use of an air sack chart, the humidity can be adjusted to get the right size of air sack for a successful hatch. The picture of the egg shown is at day 8 of the incubation process and the air sack is still quite small.
As you can see, it is very hard to answer the question of why ducklings sometimes die fully formed in the shell but hopefully this article has given you some areas to investigate and thoughts for improvement. It never ceases to amaze me how wonderful mother nature is and if you continue to have problems, maybe incubation using a broody hen would be the answer next year?