Are you supposed to crate the puppy every time it's unsupervised? In other words, is it locked in when you take a shower, go shopping, go to work, and sleep for the night? I can't imagine that would be healthy. I'd be afraid crate training would make the pup leery of coming when called, but I'm not familiar with the practice. I'll check the blog here to see if there's an article about it.
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I would be upset with any professional who pushed an opinion on me that made me uncomfortable and wouldn't go back. If you've found a way to housebreak your puppy that works for you then stick with it. Consistency is the key to housebreaking a pet regardless of the method you use.