1.Do you know what it is about Fynn and Joker that she doesn't like - is it their style of interaction, or is it that they are male, or what?
It might be that their male. I know the breeder said 6 of the pups in the litter were female.
Fynn lays down on the ground or play bows and wags his tail as he tries to get someone to play with him. Then if that dont work he gets frustrated and barks. But I quickly tell him that's enough and he shuts up.
Joker is a little rough. He is a little mouthy but I can tell him leave it and he'll stop.
2.How long has this behavior been going on for?
Since I got her.
3.Does she only do it if they initiate contact, or does she also do it if they are just in the room with her?
She snaps at them if they try to play with her.
If they are in the room with her she will hide somewhere.
4.What is she like with OTHER dogs that she meets when out walking, or at puppy class? Does she have preferences there also?
She doesnt pay attention to other dogs. If they try to smell her he walks away to the nearest human(at class). On walks she just walks beside me or Samantha looking at us the whole time. It's like you tell her to "watch me."
5. Have you done anything to ease the relationship between them and help them get along (example: feeding both high value treats when in the same room, crating the boys so Sinder gets some freedom without harassment and gets used to them, as you might with a cat who hated a new puppy, rubbing an old towel over Joker and Fynn and putting it in Sinder's bed, or under under dinner dish before she eats, that kind of thing?)
Well the crate she's in is Joker's old crate. And it smells like Joker because there's a towel in it and I use that crate for Joker when we go to class once a week.
I do give her some alone time where the others are crated. But then she's usually asleep on the couch or playing in Samantha's room, where the others are not allowed!