If no hormone problems & pcos is ruled out & the obgyn tells you to see an endocrinologist...What could be the cause for secondary amnorrea?

Not sure. Since the menstrual cycle is controlled by hormones, i don't understand the comment. Your physician recommended you see an endocrinologist which sounds like a good idea.
Several possibilitie. It sounds like you need to see the endocrinologist. Possible explanations might include hypothalamic amenorrhea, non-congenital anatomic issues (e.g. Asherman's/scarring), or other more rare conditions.