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 latter is the most common reason for BTB in the initial three months of birth control pill use.
In terms of the dark brown color, 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. The protection from pregnancy is still in 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.
Yours,
Jane
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