we had that for a long time (his breath too), but it has gone back to normal since we started doing baby acidophilous every day. for us i think it was a sign that his tummy flora was a little out of balance.
My baby's poop has smelled like this for a while now, so we went to an ND. We've had him taking probiotics 3 times a day and 30,000 IU of Vitamin A for about 3 weeks now. It's much improved and his poop is close to normal.