I think it is actually a lot more common than you think. Words of affirmation are often very important to people and women in particular (IMO). My W is a wonderful mother, wife and is still smokin hot at 39. However, she isn't happy either.
I think that the self esteem issues start early and can come from anything. I would continue to be positive. Tell her all the good things she needs to hear, but don't go too far with it. Be honest and positive.