If she's always been this way, for the past 7 years, I can't be sure there is going to be a quick easy fix. I know you said she had a full work-up at the vet, but did that include any labwork? Blood tests to check for things like kidney disease or diabetes? And a urinalysis?
Is she the only cat in the house? I always recommend 1 more litter box than you have cats. Usually cats like boxes that are uncovered but not all. They usually like the soft sand-like clumping/scoopable type litter that is unscented. They also like having a box that is large enough to hold them if they are stretching out to scratch and dig in the litter. With the scooping litter, I recommend scooping out any waste 1 to 2 times a day, and then dumping the whole thing once a week. She may like a different kind of litter, so you could try different litters in different boxes and see if there is one she goes for more. There is a litter additive called Dr. Easley's Cat Attract that you can add to the box and see if it makes a difference. It's good the boxes are out of the way, but they shouldn't be so out of the way that it's inconvenient for her to use them. For example, if they are down in the cellar, and she's older, it may be getting harder for her to use the stairs.
If she's a Persian, she may be getting litter stuck in the fur in her paws and around her back end. If she is not good about keeping herself clean, have her coat clipped or shaved down shorter.
In the end though, if her preference is to go in places that are hard flat surfaces with no litter to dig in, that may just be the way she is. You could always try having a litter box with nothing in it and see if she goes in it. Another option would be seeing if your vet can refer you to a behavior specialist if everything else medically is normal.