Cats will very commonly stop using the litterbox when they have health problems because they associate the litterbox with their source of discomfort. Health issues can pop up fairly quickly, even something minor like a UTI, so I would recommend bringing her back to the vet to have it checked out.

As Karen pointed out, using an enzymatic cleaner for the urine spots is also really the only way to clean them; if its behavioral and you don't use an enzymatic cleaner, she will continue to urinate in the same areas because she can still smell it.

Good luck!