in my own experience i get stomach cramps, stiches, and spurious annoying abdominal pains or aches while running if i have had a lay off from training for wahtever reason. i read once that all the organs, especially the liver, are heavy and the tendons/ ligaments/ fibres which bind them need to adapt to a running regime.....
I think you are more prone to stomach cramps whilst running if you are tense and not relaxing your body and your breathing. I'd also advise not to eat anything 3 hours before you run.
What you are probably experiencing is a spleenic contraction or a stitch. This is caused by not enough oxygen getting around the body. Take deeper breaths, and breathe correctly in order to prevent this. As you get fitter this gets better.