I found a site: http://www.dogsadversereactions.com/...edisposed.html
that may help you decide what to discuss with your vet. I'm not one, but it sounds like a possible auto immune problems starting.
A few books :" Vaccine guide for dogs & cats" by Catherine J.M. Diogati, MA
And one "Herbal dog care" by Randy Kidd, DVM,PhD are also helpful.
If you ever plan on breeding please be aware of what happened with your dogs and let prospective buyers of your pups know about it.