Has the thyroid been checked? Not common to have a really low thryoid in young dogs, but it happens, and has been said to be more frequent.
Has the pup been checked for tick diseases? Have the parents ever had a tick disease or live in an area where they are? If a pup is born with it, it may not register antibodies.
I would want a full blood panel run, including T4 thyroid, and would ask for a copy and look carefully to see if anything is at the high and low ranges.
I would also want a chiropractic evaluation: www.avcadoctors.com
Anything neurological will be made worse if the spine is not correctly aligned.
I would also hold off on any future vaccinations until this gets figured out.