For me, it was the extreme and sudden increase in fiber that my digestive system was not used to. Before starting the diet I was a complete "carboholic" 20-year-old (otherwise healthy and only 10 lbs. overweight) eating copious amounts of bread and bad carbs, and very little veggies and fiber. All my life, whenever my intake of fiber was significantly increased, without also increasing the bread/starch intake, I would get diarrhea.
So I already understood the cause when I suffered your same exact symptoms during Phase I, but I severely underestimated the outcome! It was so bad, I was almost fired for taking such long bathroom breaks and lack of concentration due to my stomach pain and discomfort. Not to mention the extreme gas and embarrassment!
Of course, not everyone has these symptoms when increasing the fiber, so it is probably a combination of increasing the fiber too SUDDENLY, just having a sensitive stomach in general, and/or an imbalance of digestive enzymes/bacteria. My symptoms subsided with the Phase II foods, but I'm sure that if I had just taken a more gradual approach right before beginning Phase I (let's call it 2 weeks of "Phase 0") slowly eliminating all carbs, while slowly adding more fiber, I would have been fine during Phase I.
That was a couple years ago and I am trying to get healthy again, but this time I think I'm just going to skip Phase I all together. Good luck, hope this helps.