
Fading Puppy Syndrome is a term loosely used to describe a number of conditions - there is, I think, a thread on here somewhere written by Admin if I remember correctly about Fading Puppy Syndrome but I cannot find it at the moment.
I have not personally experienced Fading Puppy Syndrome, but thought that it only was applicable during the first 14 days of a pups life. It could be that the pup has a congential condition, some conditions only come to light once weaning begins. Or you need a little longer to see if the second course of antibiotics are going to work, there should be some signs of improvement usually within 24 hours.
This is not a lot of help, do not know of anything else to suggest.