I think the girls are right by suggesting that you have an open dialogue about how she is feeling. Just approach it as "Hey, now that you are back to work full time for a little while now, I was wondering how everything is going? How have you all settled in?" That gives her an opportunity to voice any concerns that she may have. You already have an idea of what it is that she doesn't like/feel comfortable with, so hopefully nothing catches you off guard. Either way, keep your cool and let her know that for the relationship to work, she needs to trust that you are taking the very best care of her little man.
If she asks how he is settling in; tell her honestly that he is still having some challenges, but that you feel that it may have something to do with her feeling uncomfortable.
Good luck, and let us know what happens.