Could it be a side reaction to the antibiotic? They can be very harsh on stomachs. And that maybe with the food change. Could you try putting him back on the bland diet while he is on antibiotics?
Also make sure that he is drinking enough because puppies can get dehydrated quickly.
I don't have that much experience with this type of situation so hopefully others will chime in too.
Poor little guy...I hope that he gets better soon.