Well, even though marketing will tell you otherwise, birth control is hard on you, just like any drug. That's why nature is not taking its course: you're going from one thing that messes with nature's course to another. The good news is, fixing it is very much in your hands.
The best thing you can do is a more natural approach to both birth control and your body in general. So, get off provera, do some gentle cleansing, eat a healthy, non-packaged-foods diet as best you can, drink plenty of water daily, and see an acupuncturist to balance out your hormones. Also, make sure to get plastics and chemical cleaners out of your life. They mess with hormones (this will be important for your little boy, too). So, for example, don't store food in plastic. Use Pyrex or Corningware, and use waxed paper instead of plastic wrap whenever possible. Get the vinyl out of your house, too. Check your blinds. Are they vinyl or metal? If vinyl, toss 'em! What about the shower curtain? Replace it with fabric, and you can use a fabric liner, as well. Etc.
Good luck. And, really: dump the provera (but NOT DOWN THE DRAIN :) and go see an acupuncturist.