Brown Discharge after period

Hi im 21 yrs old and engaged.  My Fiance and I have not had sexual intercourse in over 2 months.  I stopped taking my birth control in May mid cycle becuase it was not agreeing with me.  I got a pill period a few days later, and then the next month got a normal period, I had protected sex one time that month, and my period was almost 2 weeks late the next month.  I got my period have not had sex all month and got another period this month, it was a more light period then usual just like the last 2 I have had off the pill.  The first two days were heavy and then it was light, they usually last about 7 days and then I get a few days of brownish discharge after that.  I am still having brownish very little discharge it is like a light brown and its just on and off, not every day just once in a while but I have also had some cramping and bach ache and have felt a little pms like.  I have had cysts in the past could this be what is going on?  What could the brownish discharge be from because I have not had sexual intercourse in over 2 months and have had 2 periods, so I am not really worried about being pregnant, but something obviously is not right... any help?