I didn't have a single GI issue during the first 30 days of Paleo. To be honest, I didn't feel any drastic improvement like people claim here (and I didn't cheat). Towards the end, my stress levels from work were really bad + slight depression caused a bad stomach upset. (I have had exactly similar issues before due to stress). Its been almost two weeks now and the GI problems persist. Lately I have started to get stomach pains and it sometimes wakes me up in the night. So I did what I used to do before - give the stomach some rest. I ate rice + yogurt (low fat + easy to digest) yesterday and the pain pretty much disappeared (shocking isn't it?). I again started eating meat today and the pain is back. Could be that I am not able to digest fat. Digestive enzymes didn't help much. Basically I am looking for stuff to eat which is very easy on the stomach and do some fasting kind of gig to give my stomach some rest. Muscle loss is a concern for me so it will be great if I can get back on track quickly.
When I have stomach/intestinal issues, I do a 3 day bland diet. You will probably feel better at the end of day two, but for me, I need to keep going through day 3 otherwise the problem will resurface. Bland foods include rice, unsweetened natural apple sauce, and bananas. Many also do boiled chicken with no skin and its broth. And water. DO this for three days and your stomach will have time to recover. On day four, you can ease back into eating more normally. My suggestion would be try this route and see if it works before trying anything more drastic. If your intestinal tract is screwed up, then you will have trouble digesting all kinds of things. That does not mean all those things are bad for you or that you can never digest them, it just means you can't digest them when your intestinal tract is all screwed up! However, if you keep having the problem over and over, then you should probably consider excluding things one at a time to see if you can determine if there is anything in particular besides just stress that might be exacerbating the problem.
You might be interested in the soup I devised to clear up stomach issues http://huntgatherlove.com/content/hangover-soup
When I get myself in such a situation, pumpkin, apple sauce, banana, tapioca, sweet potato, and other such bland foods work wonders. If rice works for you, you might try arroz caldo. The combo of broth + ginger works some magic I think.
It's hard to tell but your body might be doing better with a bit of starch, which you got from rice.
Cleaning up your diet might have let some underlining condition show up its face a bit. If you have a problem with fat, you would have seen it before, unless you never ate fatty meals before going Paleo.
The probiotic in the yogurt might have helped a bit too curtail whatever problem you might be dealing with, though I doubt you would see a big relief only from eating yogurt once. I would try doing the Paleo approach, taking a good probiotic and including a bit of starch from sweet potatoes and see how it goes.
Not sure if it is your issue, but when I had something similar (would wake me at night), I traced it back to constipation (was going very heavy in the meat side at the time). Tossed in more veggies and started taking magnesium helped resolve it for me, although I still have the tendencies if I'm not careful.