With bad breeding, I'm asuming that the breeder didn't check out the lines (like a BYB or mill would do).

That's what he said. But I have to wonder how many other puppies from this breeder has the same problem. It could be an isolated case but since we didn't keep in contact with her, who knows.
At first, my mom thought she was having seizures. I kept Lily for her when she went to Colorado. Then I noticed the same thing...head shaking or bobbing. Not for a long period of time...maybe around 20 seconds. She was fully awake and her body didn't stiffen. I told mom to get her to a vet and have her checked out but that I didn't feel it was wasn't seizures.
Lily's condition hasn't improved but it hasn't gotten worse either. She still has her episodes. Don't know what kind of tests were run because I wasn't there at the vet's. Mom lives out of town.
Also wanted to add that Lily is a year old this month. My mom started noticing her episodes around 5-6 months of age.