Dear Jen,
Of course you were regular, when taking the Birth Control Pill and artificially regulating your cycle. Your natural hormones were not responsible for this, like now!
Infertility is a common side effect of using the pill. Its use ages the cervix faster than normal and may result in hormonal insufficiency for some time. The severity of effects varies from woman to woman. Through charting it is possible to recognize cervical mucus of good quality (indicator of fertility) or identify abnormalities in the cycle, in your case the unusual tail end brown bleeding which is usually due to inadequate progesterone support of the endometrium (the lining of the uterus) in the luteal phase of the previous cycle. That can cause the irregular sloughing you see at the end of menstruation.
Other possibilities for this type of bleeding may be thyroid dysfunction or infection. You may want to ask your doctor to rule out these possibilities.
Due to abnormal growth or development of the endometrium there is increased risk of miscarriage. The levels of progesterone hormone should be measured in a timely fashion to assure proper maturation of the endometrium. It is not enough to just take one measurement. A series of tests should be done during the post peak phase of the cycle using your chart to determine the correct days. The charting information will be invaluable for diagnosis and treatment of this unusual bleeding. Timed progesterone treatment may be the key to the return of fertility for you!
A good place to start would be to find a FertilityCare Practitioner (listed in this site) for the charting assistance you need.
Angie Frausto