This pain is caused by irritation of the nerves around the stomach and intestines.
The stomach and intestines are lined with nerves that transmit pain. When we eat, a large amount of blood flows into the stomach and intestines, stimulating their movement. This is because it takes a lot of energy to digest the food we eat.
However, when you run, the blood goes to the muscles, which causes only a little blood to flow to the stomach and intestines.
When there is a lot to digest in the stomach and intestines, but only a little blood for energy, the stomach and intestines start to cramp because they do not have enough energy. The nerves around the stomach and intestines feel these cramps, and this is what causes the dull ache.