It sounds like your body is still getting into the swing of menstruation and hasn't quite got all your hormones under control yet, hence the irregularity of your periods. As for the brown blood, it is completely normal.
Here is a good website that explains it

http://vascular-events.com/fluid.aspx

I am 18 years old and have been on the pill since I was 15. I had a boyfriend then and am still with the same one, and we have had sex basically since I began the pill, and have sex maybe once a week, if even. I have almost NEVER skipped a day, and take it religiously. Sometimes, I even skip my placebo/sugar pills and take the regular white pills so that I do not get a period that month. It is now April, and I had my last period in maybe Febuary (I took my pill all through march to avoid a period during a vacation). Four days ago, I began my placebo pill in order to have a period, but instead I have what seems like dark brown blood. I am not sure if this is just because my body has to sort of "clear out" or if it is something more. HELP!