There shouldn't be any smell to your eggs. Do they smell rotten? When did you candle last? Did you open your vents at lock down, up your humidity to 65% or 70%? Is this a still air or forced air incubator? What temp did you run throughout the cycle?
We will need more info to help solve this mystery. You can also post questions in our Incubating Eggs forums for more input on this as well...