Recently I had a client ask me about why she was having side cramps from running when she felt like she was in decent shape and was working on making sure her breathing was rhythmic and not erratic.  She is training to do the Pikes Peak Ascent and so she is mainly trail running and normally has the side aches when she is running downhill.  I explained to her that it could be that it is not a side ache at all, but that she could have a weak core, or tight hip flexor muscles that could be bothering her when she is running downhill, which could feel like a side ache but is a different issue all together.  Along the same lines it could also be a form or posture issue that is over-stressing her abdominal muscles and causing the discomfort.  It could also be that some people tend to hold their breath for a few strides as they start running downhill, especially on a technical descent which could be enough to cause a side ache even if you attempt to regulate your breathing pattern after that.  The only way to be sure what the answer is to this is to have a fitness assessment and/or a technique assessment by a trained individual.