It usually takes about 3 weeks to a month for your body to adjust to a new long-term medication. Especially birth control pills. Thats why they tell you to use protection the first month on starting the pill or switching.
Yes, the cysts could very well have something to do with it. I would definatly call my Gyno and have them evaluate your pills if this continues in the next few weeks or again, it could be the cysts.
EDIT: It's amazing what your body goes through after having a baby. I have had 2 boys and also had miscarriages. Horomones are a crazy thing. But then again, they are an excuse for MANY things we do... even if we do mean to do them