It could be you don't notice it after a while or it could be you are using the Aroma Stone incorrectly.Is it one of the shallowwhite ones withcircular ridges on it and straight sides? If it is and if you are not using it with water, citrus oils should be placed near the edge where it is cooler than in the middle of the burner. Or you could use it with water, that usually slows down the evaporation rate. They used to give out quite detailed instruction with this model about where to place different oils on the dish.
I'm not familiar with the newer rounder ones, but the same element design may be used, so it might be worth trying placing the oils out towards the edge, or trying it with water.
It could very well just be your nose becoming used to the smell after an hour, just the same way some people will pile on the perfume and then they think it's down to a nice subtle note and every one else thinks they reek.