What Causes Brown Vaginal Discharge While Withdrawing From Contraceptives?

I stopped taking birth control 2 months ago. And after being a week late last month I had some brown vaginal discharge that didn't smell and went away after a couple days. Now I am again having brown vaginal discharge but this time it is clumpy. Is this some type of period and if not what do I do to get rid of it? On a side note my doctor prescribed me flagyl in December because she said I had bacterial vaginosis. I finished the antibiotic and now this is happening.