I had a similar thing happen to me along the way on my search. I could sense something wasn't quite right near the end of my wait and I believe the breeder decided to keep the girl I had picked or sell her for more cash.
I think a good breeder would not want to send you a puppy with an eye infection and would let you know what happened, but would just treat it and give her to you when it has cleared up (a week later than planned or something). No ultimatum of sick puppy or no puppy.
Anyway, good luck on your search!
