Oddly, I'm seeming to have the opposite experience. Omeprazole 20 mg was working great for me for two years, no acid reflux, no weird side effects. Then I ran out for a week or so and started taking Protonix 40 mg that my mother had, and I've been having upset stomach, sore throat and sharp stomach pains since. I'm stopping the Protonix and taking nothing at all until I can get some more Omeprazole, and just hoping I didn't do any permanent damage by switching back and forth between the two.