Warm humid eggs DO have a smell. Plus, if there is any odours left over from the last hatch, they will get really strong in the next one. Please don't think I'm suggesting you haven't cleaned it well! I use a solution I got from my sister (a vet) that kills all bacteria, moulds and yeasts. They use it to sterilise the clinic and theater, and it is even used against airborne bacterias and viruses. It's fab. I spray it all over the bator, lid included, rinse out eh bottom and trays and let it dry in the sun outside. The pack it up and put it in a sealed box until next time. I use water from the kettle, cooled, like for a babies formula bottle. I have well water too, so it's untreated and while absolutely YUMMY I wouldn't put it in a bacteria haven like an incubator straight from the tap, especially the hot tap.
Edit: for darkmatter - what's your view on the use of formalin? I have some 30%, also from my sister, as a post hatch cleaning agent, it says (in the bator instructions) to put some in the bator and bring it up to temp after hatch is done and a basic clean with water has been completed. Am a bit wary of using it, how long will it take to dissipate, and do I really need to have something so toxic around?