Have you taken a stool sample to your vet? It's possible she might
have a parasite that is causing pain, and she's searching for another
place that isn't painful. This happened to our kitten--she had
roundworms and coccidia. When that cleared up she used the boxes again
regularly.

Can you try another type of litter to see if she likes that better?
There are lots of litter types now. She might like one that is
"scoopable," so the urine doesn't seep to the bottom of the box.

Rene