My Pix had diarrhea about 3 weeks ago, and the vet prescribed antibiotics. From the day she had the last bowel movement, it took her almost 5 days to have the next. Don't worry, I called my vet with the same concern as yours, and she told me it takes a few days for anything new to be formed in their digestive systems. I also fed her rice and boiled chicken for as long as she was on the antibiotics.
Hope your baby recovers in no time!