A lot of people seem to hurt on their right sides. Some hurt up but I think most hurt lower down, like you.
The nasty thing about IBS is that it seems to get worse around a woman's cycle. Apparently the hormone fluctuations have something to do with it. If you are prone to ovarian cysts, then I would think your hormones are off so you may have even more IBS problems because your hormones aren't right.
Are you on birth control? I was under the impression that they used it to help treat cysts at any rate, so if you're not on it ask why not. I'm on Depo Provera which keeps you from ovulating all together. Maybe it would help decrease your cysts?
Then again, you may have a "female problem" that is hitherto undetected and it is causing your IBS symptoms, including bowel problems. My mother and stepmother have both had hysterectomies after a long bout of pain and illness, but unfortunately I don't know what their symptoms were beforehand. If you have a family history of "female problems," be sure to tell all of your doctors.
Did you have IBS symptoms before you had the ruptured cyst? And for how long?