Spotting for over two weeks

Wondering if anyone else has experienced this. My doctor believes I have a hormone deficiency and I started birth control pills over a year ago. I used to get terrible migraine headaches, cramps and heavy bleeding, so I started on BC to help. Which for the first 8-9 months, my symptom intensity lessened. But then after then, my symptoms went back to normal and still had intense cramps and headaches. My doctor told me that she'd like me to try skipping my periods. So instead of taking the placebo week, I would start a new pack. I have now skipped two placebo weeks and have experienced heavy cramping, headaches and spotting for over two weeks now. Over the weekend I had somewhat heavier bleeding, enough to soak through my jeans. Occasionally when I use the bathroom, I notice a foul smell that just isn't pleasant. Has anyone experienced this or have any pointers? Is it time to call the doctor or will it pass since my body is still getting used to this?