When a hen squats, and makes herself flat, she is being submissive. Three hens to one rooster is a low ratio, and I'm surprised all of them don't look barebacked and raggedy. One thing that helps is a hen saddle. Of course, that doesn't help if the roo pulls out their neck feathers and the feathers on their heads.
Unless you are breeding, I wouldn't keep a rooster with just a few hens like that.
Also, sometimes a rooster just picks a hen out that he doesn't like, and now matter how flat she squats, he abuses her. Unnecessary roughness. I would get rid of him. If a hen is running from a rooster, he is being too rough. That's making her miserable, I bet.
Sorry this is happening for you, I know you can get attached to roosters too, and they are so pretty......I've had two roosters so far, and I've given them both away because they were too rough on the girls.
I also had a nice Wheaten Marans rooster, and he was just STUNNING! Anyhow, I had two hens (breeding trio). He really favored one hen and mated with her so much that her back started getting bald and she had a few sores. I put a hen saddle on her, which helped, but he pulled the feathers out of her neck too, and she was just a mess.......And she was sooo pretty when I got her. I like pretty hens. I gave the trio back to the breeder.
I have a rooster now that I hatched myself. He's an olive egger. Anyhow, he's as sweet as pie so far, and I sure hope he stays that way.......
So I hope you find a solution to your problem that makes you happy!
Good luck,
Sharon