She barked at him when he got home and he threw some treats, when she would come near her, he would give her treats. She would take treats from his hand and then back away and growl some more. She then started following him around the house, growling/barking and then looking at his hands as if she expected treats. She barked all through dinner. She then sat on the couch with me and allowed him to sit next to her, but continued to look at him and growl at him occassionally. He finally gave up and went to bed and she stopped barking.
This will help you understand counter conditioning. I think what is happening here is the treat is coming at the wrong time plus don't have him hand it to her that is to confrontational. Just have him casually drop them and move on. No eye contact just become a treat machine if she is not growling.