Ovarian Cysts, believe it or not are actually quite common in women and most of the time are harmless. Some women never actually realize that they've had a cyst because many times they are not bothersome and will disappear on their own after a couple of months without treatment.
You may not have any symptoms, but remember that if you get an abrupt onset of pain or pain accompanied by fever and/or vomiting-- you should see a doctor.
Good luck, I know it can be frustrating not knowing why your period is irregular but you may really have nothing to worry about since your labs are perfectly fine and you have no other symptoms of illness. Again, a second opinion never hurts.