When I brought Rusty home, he had the same problem for about 3 days. I think that it is the change in environment. I added boiled chicken and rice to his kibble and switched to bottled water. The diarrhea went away quickly and he was back to himself. Just becareful that he doesn't get hypoglycemic, have some nutrical/karo syrup nearby. Also, that he is drinking enough water.
Hope your baby feels better soon!