If you have always had painful menstruation, you are more likely to experience pain with progesterone withdrawal bleeding as well.
It may be that you have had undiagnosed endometriosis all this time, or are simply unlucky to have more pain with uterine bleeding than others.
Having banked 20 years' worth of risk reduction for ovarian and endometrial cancer on the combined pill (which is also my personal goal) you are actually in a relatively favourable position now.
There is a clear history of undertreatment with progesterone- guidelines recommend 100 mg every night vaginally not alternative nights, and bleeding precipitated by a missed dose.
Therefore if you start taking it in accordance with guidelines, this is likely to eradicate the bleeding, and with it the pain.