i have two theories relating to this subject... one refers to running, the other to apnea
1. while running, (or generally doing anything strenous, where one has to carry his bodyweight) it has been shown that our bodies attempt to reduce our weight as much as possible, it does this in one of three ways: urinating, deficating, or vomiting. this seems to be an "animal instinct" that our predecessors left us with. this has also been noted in animals, when being chased animals have a tendency to do one of those three things.
2. while in apnea i think that the need to go deficate is related to the increase pressure in the abdominal area, (as per what Pezman said)
actually, it looks like i have another point also...
as for soldiers "commonly" losing bowel control (first off im going to have to disagree with the commonly part... i havent seen it done yet, but i will see after my infantry course this summer), as with point #1 we have to carry a heavy load (well, what do you expect, we live out of our rucksacks...) and when we need to hurry, our body tries to lower the weight we have to carry as much as possible
cheers