Has she had her Bordetella ? was it in shot form, or through the nose ? if it was through the nose that could be the problem with her nose. It can cause cronic rhinitis, unfortunatly I learned that the hard way.And there is no cure only treatment, talk to your vet about it. So if anyone else is reading, stay away from the through the nose vacs. You can use digestive enzymes on her food to help her absorbe the nutrients from her food better. For a dog her size just open the capsule and sprinkle a tiny bit on her food every time you feed her. If her coat gets greasy , cut back on it.
If your vet has done blood work, she's probably fine , she's just going to be a tiny dog. Remember they have little bitty bellies and thats why they need to be fed 3 to 5 times a day when they are growing. Good luck with her.