are you using protein shakes?
if you're increasing your protein by using whey or soy shakes, that may explain the bloating. i know whey protein powder in particular can cause stomach discomfort. also, some people have sensitivity to soy so increasing soy might cause problems.
if you're eating more meat, have you decreased your fiber intake? meat has no fiber so if you're replacing other foods with meat, you may need to make a concerted effort to get fiber elsewhere.
if you're getting your extra protein through dairy, that could also cause problems if you're lactose intolerant, which most of the population actually is.
these are just some suggestions--i've never heard of protein intake by itself leading to stomach difficulty.