I'm having this exact problem right now. My doctor has prescribed a proton-pump inhibitor and is having me get an upper GI to check for ulcers. The PPI is helping although I still have some stomach pain. I'm tapering down, so I hope the stomach pains will start to recede.
I would definitely talk to your GI about taking an acid reducer or PPI.
Hope you feel better,
11 years of UC
Currently taking: Asacol, Rowasa, Canasa, Humira (started 4/11), tumeric, ginger, boswellia, slippery elm, VSL#3