You're not breathing from the lower part of your lungs. Put your hand on your stomach and breathe deeply. If you're breathing from your lower lungs, your stomach should rise and fall. Practice this even when you're not running in order to bring your body accustom this using the deeper parts of your lungs. If that makes sense.
Other things come into play such as how fast you start off, how long between eating , sodium levels, blah blah. Treat running like swimming. Give it some time between eating and running.
Here is a link that will give you some info about it and hopefully some ideas to help give you some releif. Hope it helps.