Any ideas on what could be wrong?

You need to see a new doctor! You know your body and what is not "normal" for you! Black stool is NOT normal! Even if the discomfort is not gastrointestinal, any prolonged pain should be investigated. It could be uterine pain, and checked out by an Gynecologist. When you visited the ER, did they do any ultrasounds or x-rays of your abdomen? Discomfort bad enough to get you to the ER should be investigated beyond a regime of antacid tablets! IBS is very common, but it can also mask other conditions. As I said before, you know what your normal is. Either way, you need a second opinion!