If it's not a cyst, then it's quite possibly ovulation pains. Take some Midol or whatever pain killer you typically use for cramps. If that doesn't work, after a safe amount of time, try some other one.
It probably IS a cyst since women form them when we ovulate anyway. They're supposed to go away in a few days when the egg finally ruptures through during ovulation. Most of the time we never notice when it happens. I usually knew exactly when I was ovulating and on what side. It was uncomfortable, but nothing like the pain of a slowly draining or ruptured cyst that's been cooking for months. You may be just one of those "lucky" women who can feel ovulation when nothing is wrong.
Is your doctor saying he can't feel any cysts or has he been doing regular transvaginal ultrasounds to check? Did you ask him about your symptoms?