This is a long shot... My mother has problems with her eyes. Nothing serious, but she refers to them as her "little bugs". She can see fine, except for these little dots on her peripheral vision that move around when she shifts her eyes. They look like flies that move off when she tries to look at them. Maybe your dog is having a similar issue. Since she's afraid of flies, it might look like there are flies constantly just out of her field of vision. Because the basement is dark, she doesn't see the flies anymore, and so is more comfortable down there. Like I said, it's a long shot...
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