Dear An: Thanks for the helpful history. It sounds like your GYN suspected that the bleeding prior to birth control pills (BCPs) was caused by missed ovulations. It also sounds like you got a good work up to look for all the varied causes of erratic ovulations and prolonged bleeding (eg ovarian cysts, PCOS, fibroids or other problems inside the uterus, and probably blood tests for low thyroid).
In terms of the current bleeding, my best GUESS is that you are experiencing breakthrough bleeding--also known as "poor cycle control". Alas, breakthrough bleeding (BTB) can be a common side effect of most types of hormonal birth control (eg pills/patch/ring/shot/Mirena IUD). Among birth control pill users BTB frequently occurs after a missed or late pill. In your case it sounds like you are careful to take pills at the same time daily. More remotely, BTB in a pill user can arise if she has gotten a chlamydia infection--not an issue in your situation.
When a woman uses hormonal birth control it can make the lining of the uterus more unstable--so it is easier to have some of it begin to shed. Sometimes the lining is less stable because the hormones make the lining much thinner (actually this is good as a thin lining is a healthy lining). Sometimes the lining is unstable because the hormones can make parts of the lining out of synch. This later reason is more common within the first three months of birth control pill use.
In terms of the dark brown blood, when the bleeding is brisk and heavy the blood flows quickly out of the uterus and vagina. When the bleeding is scant and slower it has a much longer time to be exposed to the oxygen in the air. This exposure will turn the blood color brownish. Think about a piece of meat which has been exposed to air for a while. The outside will be dark brown/gray. Yet when you cut into the meat, and expose an area which has not been in contact with the air, the color will be red.
It is very common for women using birth control pills to have a "period" which looks more like dark motor oil sludge than bright red menstrual bleeding. The synthetic progesterone in the Pill creates a thinner lining inside the uterus. This creates a decreased amount of flow. This more scant flow will appear as a dark brown color, and thick consistency.
Bottom line, BTB on hormonal methods of birth control is a nuisance side effect.. If your poor cycle control persists you should return to your GYN or clinic. Often a change in the brand, or formula, of birth control pill will fix the problem.
Congrats on losing that 60 pounds despite MANY other health related stressors! You are to be lauded and we hope that the next six months will be better than the pasty six months.
In Admiration,
Jane