Since any medical conditions have been ruled out - there are other reasons why she chooses to behave this way. However, figuring out that reason can be a daunting task.
But here are some ideas to consider:
1. Does she like her litter box and the litter-type it contains? Often cats can be sensitive to certain litter-types as they do not like the feel of it on their paws. She maybe trying to tell you so when she meows.
She may consider the litter box itself to be to small for her. Ideally, a litter box should be one and a half times the length of an adult cat, from the tip of the nose to the base of the tail. This ensures plenty of room for the cat to make a full turn comfortably without the feeling of being cramped.
2. Consider the location. If there have been any sudden changes or if the litter box is placed in an area she is uncomfortable with...may play a part in her avoidance.
3. This could also stem from her earlier years. If she was taken from her mother at to early of an age, she likely was not properly taught. These things do come instinctually but are usually first guided by the mother.
Best to keep her routine consistent. If you decide to make any changes to her litter box or the type - be sure to make the transition gradual.