what Lise said, and also it could be from the exertion. Esp. if you are really ramping up the effort and your body is not ready for it. Can also be an electrolyte embalance, so make sure your sodium is in check.
Hopefully it's not *female* related, but I'm guessing not if it only happens on certain runs. Sounds like your body needs to adapt to the effort. Once your fitness improves (not saying you are not fit. Just that your body may not be used to the effort) I would guess that they would go away.
I got a side stitch today on my run after my long ride, but mine was from lack of sodium. As soon as I got some salt in me it went away. When you get them do you push hard into the cramp w/ your fingers and then expel your breath with force? That usually loosens it up for me. You can also poke your fingers into the cramp and kind of lean into it while breathing hard.
Hope this helps??