This is going to be a really dumb question, but there's normally a tight lid on that egg tub, right?

That aside, you are correct about condensation -- you won't see it when everything is exactly the same temperature (which is theoretically possible in a home incubator) or there is air movement. Air movement in an environment that feels very humid to us as humans still causes moisture to move around. So, you'll have areas of higher or lower humidity and the levels will not be constant.

With substrateless incubation, eggs stay plump up until the final weeks because, ideally, they are in a box of close to 100% humidity. Barring any other factors, your eggs are deflating because they are losing more moisture than they are gaining from the air. When it comes down to choosing to believe the hygrometer or the eggs, always believe the eggs. Stopping the airflow is the easiest thing to do, which (you are using a lid, as well, right??) you're already doing. Another thing is to give the water more surface area to evaporate -- in this set up, by adding more perlite. I like to put down ~2 inches of perlite, give or take, add warm water until it just begins to float, then I set my light diffuser directly on top of it. Maybe it makes a difference, maybe it doesn't. If there is a fan in your incubator, try it turning it off. That's all I can think of off the top of my head.