I get the pulsing in my stomach too. I can actually see it pulsing - it's weird. I also have IBS. The entire GI tract is one system and when one part "breaks" usually there are consequences in other areas. 10 years ago I started to get acid reflux, drug reatment for the acid problem over time has led to other problems like IBS, weird sharp pains in the abdomen and back, stomach "pulsing", bloating, cramping, etc.
I don't think that there is anything to worry about regarding the pulsing in the stomach. My sense is that there is a lot going on in the gut when we have bad reflux and there may be inflamation causing the pulsing sensation. Perhaps it is like when we injure a part of our body, cut a finger, etc..., the area pulses or throbs in an effort to heal.