Check out what Joel E. Richter (chair of the department of gastroenterology and hepatology at the Cleveland Clinic Foundation) says about
the right time and manner in which to take a PPI: http://www.acponline.org/journals/news/jul-aug04/ppis.htm
Also, research indicates different people require different doses to achieve the same results. I was told to take mine at night because I have nightime acid, but when I have taken it during the day it works the same. I am taking 20 mg of Protonix (pantoprazole).