Hi, I'm not real sure if your saying she gets irritated eyes when on sand , or if some just gets in.
If mine get a small amount in there, you can see them kind of bulge their eye out (looks crazy) but this is their way of pushing out anything in the eye that is bothering them.
How is she getting so much in there? Is it wet where she sleeps?
Maybe like I said up top sand just irritates her eyes and she has a reaction to it.
Sandy eyes are also a sign of resp infections, but your saying this corrects itself when you take her off the sand?
Well all I can say if everything is normal and she's healthy in every other way until you put sand in the tank, then I would suggest maybe using something else in there. That would be your choice. 
Hope shes fine now!
The Kids
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PHEve / Eve