When my son was a few months old, he often had green poop too which made me worried. But his Doctor said this means that his poop has not been in his intestines for long. Aparently there is a lot of bile around the poop when it first enters the intestines from the stomach, but then the bile gets reabsorbed by the intestinal wall, and the poop looses the green color. However, if it hasn't stayed in the intestines long enough, the poop is still green.
Maybe that's what happens to you too.