you might want to go to the doctor and get checked b/c most of the time when it is the dark brown color it means it is old blood.
maybe some effect from the medication the doctor put you on, and your body is just adjusting, I would have said implantation bleeding, but it shouldnt happen twice like that, unless its just bleeding in the first trimester, which is very common and normal. calll and ask the doctor or take a test to make sure.