Are there directions that come with your medication about whether to take with food or not to? I was getting stomach aches for a while and then my doctor pointed out the giant sticker on the bottle that said, "Take with food."

If it's a new drug it might take a few weeks to get rid of side-effects, and then every time it's increased it will occur again. I'd talk to your doctor and check about whether you can take something for your stomach ache (like Dimenhydrinate) or if there is a better alternative to the medication you are taking that may cause less side-effects.

Edit: I'd stop taking things for your stomach aches, like Pepto-Bismol, because it could interact with your medication. Really, call your doctor.