[Ponyup]

I have 1 question did you notice this change in her right after the yelling episode. If not then something else has happened.
Also if it is because he's a man and she's not used to men she would of acted hesitant from the beginning. She would not have been excited to see him and suddenly go to being wary of him unless something transpired.
The fact that he got very defensive and upset when you asked him makes me think he's lieing.
I would imagine the blood shot eyes are from being hit in the face or from her not sleeping because she's trying to protect you and your daughter.

I had a small dog I found on the road. After having her for only a short time it was obvious she had been abused by a big man and that's who tossed her out on the road. It took her nearly 5 years to warm up to my dad and if a big man approached me she would go apes**t. I'm sure she was just trying to protect me and herself from danger. These little dogs remember everything and they have great instincts. Listen to your sweet baby and your heart. I would also ask your daughter her thoughts since she's around, but not has emotionally invested as you are.