I was dx w/FMS 3 years ago, but I've had the symptoms for 10. Fibro can conceivably affect any muscle or muscle group. I also have irritable bowel syndrome, which is an accompanying condition of FMS, which causes stomach cramps, among other things. While I don't have pain in my stomach muscles, I do have diaphragm issues, which is common in FMS. I get winded very easily because of my weakened diaphragm. It would be a very good idea to discuss this with your doctor on your next visit.
I have never heard of it being in the stomach muscles, but who's to say it's not possible? I have had sore stomach muscles for days just from watching a funny movie. It would be a good idea to talk to your doctor about it though, to be on the safe side.
I also have fibromyalgia but have never experienced any muscle pains in my stomach. I do know that some people have areas that are affected worse than others throughout different parts of the month, but I would check with your Doc about the stomach pain. Mine is mostly centered around my hips, knees and ankles...but I also have a more mild pain allover.