Heart burn, acid reflux is common when on a high protein diet, you can easily control it with an anti-acid of sorts. The best ones are time released because they limit / control the acidity levels. Others that have excessive calcium carbonate eliminate the sysmptoms immediately, however the heart burn often comes back with vengance. Digestive Enzymes may also help.
On a more a serious note however, heart burn (or rather perceived heart burn) is a common side effect of angina, or a build up of plaque on the walls of your arteries. If you have a slight tight chested feeling at times then go and have your cholesterol levels checked. Just as a precaution.
However the heart burn that you are talking about is probably due to a low carb to high protein ratio in your diet.