Sore and painfull for over 2 months?

My s have been sore and sometimes pain full, more in the left than the right one. Been on the pill now for 16 years. Periods haven't been normal the last 2 months. Missed 1 period and then only had a period for 2 days on the last time. My periods have always been the same lasting 5-6 days. Doctor examined me and had 2 negative pregnancy tests. Doctor said it's my hormones and nothing to worry about. Never had this before, not even when i'm due for a period. Any ideas?