Beware, this one long post.
I doubt this is the breeders doing, aside form the fact that she never should have breed these dogs in the first place. Native American Indian Dogs on the whole are known for being very fearful and aloof.
I had a Board and Train case about a year ago with a Native American Indian Dog. Same situation as you're describing. The poor dog was terrified of everything, everyone, and she'd just slink to the ground and curl up in a ball, or worse yet she'd drag her owner back home if she was on leash for a walk and something spooked her.
I'm talking full on belly-drag for this poor owner, bless her she never let go of the leash but the dog was very strong and had no intention of stopping. Someone getting their mail across the street from them would be enough to send her into a panic.
This dog was fearful from the moment they got her home from the breeder, no amount of socialization on their part or puppy classes to bring her out of her shell helped.
She was simply a basket case and it was due to genentics. The breeder could have socialized the heck out of those pups and I doubt they'd have turned out any different.
Anyway, so this little ball of nervous engery came to me for a month of board and train. Her owners were fed up, they'd tried training classes, they had a private in home trainer work with them. Nothing had helped. They couldn't have anyone over without putting the dog in another room and even then she'd freak out. If she was outside in her own fenced yard and the neighbor came out into his yard, the dog would freak and jump the fence to get away.
Keep in mind the neighbor is his his own yard and never even looked at her. And of course the horrible leash pulling which made it impossible to take her anywhere for socialization.
The first two days she was with me she never left her crate. Not for food, not for potty time, she simply would not budge, so I didn't try to force her. She eventually got hungry enough to take some turky I tossed to her, and then hungry enough to eat it from my hand. And then we could start training.
Here's a brief rundown of what I did with this dog and I'll share the results below.
All food was hand fed. She got no meals in a dish, every morsel came from me.
She was on leash at all times and attached to me. I moved. She moved.
If she wasn't on leash she was in her crate.
Once she was hungry enough to really want some turkey I taught her how to sit, then she had to sit for everything she wanted. In and out of doorways, every morself of food, in and out of the crate, before I clipped the leash on her and before I took it off. In other words NOTHING happened untill sat first.
She learned what a clicker was.
Once she learned that doing something would actually earn her either a "life reward" or a food reward she was very eager to work and teaching her basic commands came much easier. Once she knew a handful of commands I'd mix it up and ask for different ones through out the day for her rewards.
Keep in mind, even at this point I could not pet her. She wasn't aggressive, but she would shy away and try to escape if I made any move to pet her or give her affection. So our relationship was strictly a working one.
It was about day ten at this point. She was working for me well in the house and we made the switch to working outside.
She freaked out. She tried to drag me back inside. She got a prong collar.
No more pulling. We moved on. Worked on basic commands outside, taught her how to heel. And remember she's still not getting any meals, she only eats her kibble when she works for it, so she has some good motivation to pay attention to me.
Once she was consistant outside, we started taking field trips. I'll admit that I flooded her. On purpose. We heeled downtown, at the pet store, anywhere that would take us.
The first five field trips she was glued to my leg and about an inch away from having a sh*t fit. I igored her. We kept walking and kept taking field trips. Eventually, I think around the 8th one she was comfortable enough to start doing some commands out in public and actually take the kibble I offfered.
We played puppy ping pong. Which is an approach retreat game. If she's afraid of something we'd take one step toward it, stop, click/treat then turn and walk away. Turn around and go one step further, stop, click/treat, turn and walk away. And so on untill she would approach the object and sniff it.
We went on nearly twenty field trips sometimes multiple ones on each day during the time she was with me.
I never asked her to allow anyone to touch her or talk to her. In my opinion she was not and may have never been ready for that.
The results:
She was able to be out in public, pass strangers and behave in a civilized manner. She was still stressed, but it was at a low enough level that she could focus on me, run though her commands, and play Puppy Ping Pong for some kibble.
She came when called every time, she knew how to sit, down, stay, heel and leave it. She did them like a pro. But she only did them because she was hungry, not becuase she wanted to please me or because she enjoyed it. That's not what this breed is about. They're aloof by nature and you won't find one with Golden Retriever personality. They don't give a hoot if you're happy with them or not.
The day before she was scheduled to go home we were outside, I had her on a long line while she ran zoomies around me, and she came up to me and licked my face. She let me pet her and even seemed to enjoy it. I nearly cried.
She went back to her owners the next day, who had been trained in how to interact with her extensivly. They'd practiced giving commands on my dogs, on a green dog, and on several other willing furry helpers. They were well prepared.
She came back to me a month later after they admitted they wern't cut out for this long term.
She stayed with me another two months before going to live with another trainer who wanted to take her on as a project for the rest of her life.
The moral of this story? Native American Indian Dogs do not make good pets. Sure, there are exceptions to every rule and I'm sure someone, somewhere has one that's the perfect pet, but trust me, that's not your dog by the sounds of it.
Over the course of working with this dog I talked with people who rescued NAIDS and heard many stories of these same situations. Stories of NAIDS that were so fearful and untrusting that their owners eventually put them to sleep or dropped them off at the pound.
I'd bet money that the way your dog behaving is genetic, and it'll take some serious, hard core training to even put a dent in her fearful behavior. And that's something you'll have to do for the rest of her life. What I did with my B&T dog was nothing special, but it was the fact that she had consistant, clear leadership, and a clear way to for me to communicate with her that made the difference. I didn't train her for a week and then get distracted, she was trained everyday, through-out the day, and we activly worked on her fears all the time instead of sheltering her.
If you don't think you're cut out for that then I'd suggest searching for a trainer that might be willing to take her on as a project. Because it'lll do her no good to stay with someone who either cannot or will not give her the best chance toward a semi-normal life by working with her 100%
Don't feel bad if you don't think this is for you. The family who had the dog I worked with spend thousands on training for her, spent over a grand on the dog itself, spent countless hours practicing with her and learning the correct way to handle her, their dog was even fully trained and they STILL could not provide the constant, on-going training and leadership that she needed.
Not many people can. If you know you're up to the challange and you have every intention of helping her work through this no matter how long or hard it is then great, she's lucky she ended up with you. Find yourself a trainer that specializes in fearful dogs and has experience with this breed. Which might be a hard search. But they're out there.
You're average obedience trainer probably won't have a clue how to deal with this. You need someone who know how to tackle this problem specifically and has a track record of success.
I hope you're able to help your dog, but if you're not up to it, rest assured that you are not the only unsuspecting person to be taken by the "breeders" who sell these dogs. They aren't pets. They're more akin to a wild animal and you've got a lifetime of trying to tame and socialize what's close to a feral dog.
It's not fun, but the rewards if you do it right can be huge.
If you don't mind shareing, I'm interested to know what breeder you got him from. I'm willing to bet it's the same one my former clients got theirs from too.