I was hoping for some very scientific information here but none yet!

I have digestive related inflammation issues and I can tell you from experience one of the clues for me, aside from discomfort when I sit (this is when I have severe inflammation in my intestines-its hard to bend-feels like inflated balloons), I also note an increase of mucus in my bowel movements.

For me, this is a tell tale sign of things aren't going well.

I would love to see some more info on this topic!!

I am waiting for a sciency answer like Kelly too but I'll give you my symptoms.

To be accurate I can only tell you what they are from what went away with paleo and also what returns upon eating non-paleo cheats.

--Heartburn and indigestion (10 or so tums a day and heartburn meds with no relief) --Constant sore throat, phlegm and upper respiratory infections with cough --Bad PMS symptoms including emotional --The bloat!!! (Including puffy campbell kid face) --irritability and unlevel moods

For the increase in belly fat I'm not sure. The only thing i would say from my own experience is the increase in veggies bloated me daily for a time. If I certain kinds they still pooch out my tummy. Also, my belly fat went last (still going) and so it was more obvious since I lost inches everywhere else. Have you lost inches/pounds otherwise?

This is a great question, and I'm looking forward to the answers, too.

I've been doing pretty consistent Paleo for about 6 months now -- easily well over the 80%-and-you're-good guideline. Here's what I've noticed, from the few times that I stray.

1. If I indulge in something dairy -- like lots of cream in coffee, or cheese, I almost immediately get a runny nose. Not certain, but too much cream seems to give me a low-level stomach ache. Interestingly, I seem to be able to eat cheese made from milk of grass-fed cows and tolerate it well.
2. Gluten does seem to be pretty diabolical. I've only had it a few times in the past 6 months, and each time it gave me gas and some degree of bowel discomfort. It did seem to pass quickly enough, which could be because I have a lifetime of exposure to it (I'm 49), or b/c I've been so diligently Paleo that I'm able to recover quickly.
3. Sugar is also evil. Yesterday, for no good reason, I grabbed a handful of some little pecan sugar cookies that someone had brought into my office to share -- purely because they were different, and they were small. Within 2 hours, I began struggling with sleepiness. When I got to my workout, nearly 7 hours later, I had an annoying headache which didn't go away, and by the time I got home about 2 hours later, I had a continuously runny nose. All of these symptoms were gone by the following morning.

Don't know how helpful that is, but that's what I've been noticing. Good luck!