Another issue may be mental health medications. While you don't specifically state that she takes medications, if she is, they often decrease the sex drive...
I'm going to go from this from a totally different angle, one that occurs to me because of MY past. One in four women are raped before the age of 18. Many of us suppress memories because of the pain and guilt involved. When the memories begin needing to be dealt with, it often comes out first as lack of desire and guilt, followed by social anxiety. Many of us have germ issues because we feel that SA makes us "dirty". If it is a SA issue, couples counseling isn't going to help, but individual counseling for her would be...