I have a 15 week old puppy who reacts to most vaccinations by staggering and some head bobbing. This sets in about 12 hours after treatment and resolves within 36 hours. During this time, he eats normally and tries to run full out. He is a happy puppy who is growing well and is as active as a littermate that I have here. He is large-boned and has sloppier movement that his littermate, but only a breeder would notice the difference. He has a slight head bob when moving quickly but can move full steam.
I am having him tested for centronuclear myopathy but his symptoms just don't appear to be as severe as those dogs who have it.
Any help or ideas would be appreciated.

Jean Dodds is a wealth of information. Since it appears to be vaccine related, why not try reaching out to her for ideas:
http://www.hemopet.org/

I agree, contact Dr. Jean Dodds. This sounds like possible mild seizures caused by the vaccines. The head bob and sloppy movement would make me nervous. Can you disclose what brand you're using?

I had a problem with a vaccine almost 2 years ago. The entire litter was out of sorts in a couple of ways for 24 hours after vet administration. It was not the same your puppy has had but enough to say no more after the 2nd time. The name of that vaccine was Nobivac and I will never use it again! It was a buy out situation, not sure who the original company was. It was given at 8 and 11.5 weeks with nothing else around that time or changed. 8 pups received it the 1st time and 3 pups [I was vacation sitting 2 pups and had my keeper pup] for the 2nd vaccination. Same reactions both times in all pups which where intestinal, lethargy and low grade fever both times. Pups appeared miserable in that 24 hour time span. I did contact Dr.Dodds after the vet said he never heard of such a thing twice.

I have seen this head bobbing before, once with a male I owned who started the bobbing after waking up from anesthesia. It reoccurred several times after that, for seemingly random reasons. I have seen it in other Labradors also.
I had a neurologist look my dog over, and he researched it on VIN, the Veterinary Information Network. A couple of responses from vets said it had been seen in Labrador Retrievers, English Bulldogs, and some other breeds I can't remember. The responses from the vets concurred that this is actually a movement disorder (related to dizziness?), and NOT a seizure disorder. It does not seem to cause any problems and there is no loss of consciousness.
Another dog I saw that was head bobbing did so after being spayed (anesthesia again) and on acepromazine, which can also make dogs dizzy.
I don't think they know exactly what it is, and it's not very common, but seems to not cause any serious problems. I have never seen it again in my line, so am assuming it is not hereditary.
It's possible it was vaccine-induced, or drug-induced, so Dr. Dodds would be the best person to contact regarding that. Have your vet also go on VIN and look up "head bobbing."
Hope that helps!