It seems that my diarrhea becomes worst after taking Protonix. I had it under control when I was on Prednisolone alone. The PPI is taken to safeguard my stomach from upper bleeding & GERD.
You might try sucralfate, a medication which coats your stomach and helps make sure the prednisone doesn't cause irritation. I've taken it when the prednisone causes stomach pain. I'm not sure about the diarrhea; I suffer from the opposite problem.