That's another one of those 'alternative" registries that sprung up after the AKC got tougher and started requiring DNA testing, etc. The alternative registries are popular with backyard breeders and puppy mills who have either been suspended from the AKC or don't qualify. If you notice in their FAQS section, they say they are endorsed by the USDA. That is not a good sign. Large commercial breeders are required to be licensed by the USDA. Those are the breeders we refer to as "puppy mills". I notice you live in Missouri. That is considered to be the puppy mill capital of the US. Have you checked the list to see if your breeder's name is on it?
http://www.prisonersofgreed.org/ListA2006.pdf
So your puppies parents are AKC, but has to be registered with this registry? There must have been some problem with the AKC. The DNA testing could have shown the sire wasn't correct, perhaps the breeder got suspended for some reason, there could be a number of reasons why he can't be AKC registered. Have you asked your breeder about it?