You might want to consult a vet on this topic, especially if it doesn't get better with training.
As I understand it, muscle atrophy can have several causes. For example lack of use, trauma (bad fitting saddle, injury), nerval issues (lesion of Nervus suprascapularis is not uncommon for atrophy in the shoulder), disease (though it should be more of a generalised atrophy then), ...
As you describe it, my first guess would be a bad fitting saddle, or being backed without having strong enough muscles first?
You said she was away in autumn for training? How did that work out? Did it get better or worse?
If it's really just a fitness issue, I would do a lot of gymnastic groundwork with her. How is she doing with those kind of things?
Give us a little bit more details - I'm sure we can help you somehow