I'm also wondering if this could be a ruptured ovarian cyst, as the day I started seeing the brown discharge I did have a very sudden pain in my lower right abdomen but it went away pretty quick. Is it dangerous if the discharge/bleeding stops and it's a ruptured cyst?
Well, hmm. Having an ongoing issue with an ovarian cyst can affect your period, making it what my doctor just called "weird." However, an ovarian cyst usually feels a lot better when it ruptures. The reason they hurt (I'm talking about the standard kind, not a dermoid cyst or 'chocolate' cyst or any of the more unusual types) is that they are swelling and the liquid in the cyst can't work its way out. The pain would grow gradually, possibly to the point of hurting a lot, and then suddenly the cyst would drain and you'd possibly see some discharge (though maybe not, since the fluid would not necessarily go down your Fallopian tube and out the uterus). With the sudden drainage would come relief of pain, not pain.
I'd ask the doctor to try to figure out if what you are experiencing is some kind of continuing issue, since it seems to repeat. I'd especially wonder about this if you're sexually active. Sometimes the guy's penis can bruise the woman's ovary, though it would take some unusual and athletic sex to do it. If you're sexually active, also test for STDs, so you can rule out some kind of lesions in the area.
Ask the doc about doing both an ultrasound and possibly an abdominal MRI. That's the gold standard for seeing if anything is going on in terms of hyperplasia or scar tissue.
Write back after you see the doc!
I have been dealing with a very similar issue, abnormal periods and brown discharge and the works really. The doctor will/should rule out any cervical changes/cancer first. My results were negative but my ultrasound showed uneven growth of the endometrial lining. First step of treatment for this is hormone therapy. I am doing Progesterone only because the estrogen (birth control) gives me headaches but from what I've heard you will normally take both to help regulate everything. Like I said previously, make sure they do the cancer screening first because estrogen will cause cancer to grow and spread so that must be ruled out before beginning treatment. Hope this helps. All the best to you. :-)