I use to think that it didn't make a difference where the dog came from in ease of training, but after talking with Mardelen (Mary) I've changed my mind. She says that she doesn't train the pups, the mother does, and she has watched the mothers nudge the puppies over to the pee pad. Since reputable breeders keep mothers and puppies together way past the weaning period, it may be that this makes it easier to train a pup. Joey knew what the pad was and sought it out when we placed him in his playpen; if it were within three or so feet from him he would try and find it. So pet store puppies may have a harder time of "getting it" because they often leave mama much earlier, and mama is probably not trained herself. Have you tried talking to the breeder about the problem? Remember just because someone shows, it doesn't make the reputable, you can learn more about her enthusiasm for the breed by asking for her advice.
I have also read that the crate used for training must not be too large. They need to think of the crate as a bed, not an apartment, where they can poop on one side and sleep on another. The crate should be no bigger than for them to stand up turn around in. We used a small carrier for overnight training, and took him out once or twice during the night and placed him on the pee pad. During the day, unless I had both eyes on him, we kept him in a play pen with a pee pad. This site has some great tips.
Indoor Potty Training - Papers, Pee Pads, Litter Boxes and more