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I generally incubate, and even hatch in the paper trays (but cut the tips off both the cup, and the support posts). I think it helps to maintain more constant humidity, as well as temperature. The tray is a good place to spray extra moisture, especially during the last three days. I've noticed better hatch rates, and that the eggs in the middle (I stack the trays) hatch faster, and nearer together. So much so, I will put an extra layer of trays on top, when possible. I think with my incubators, I get too much airflow around the eggs, and they are dryer, even though the overall humidity is good.
Are you stacking in the hatcher or just in the incubator?