Cystitis (inflammation of the bladder) can be a cause apart from kidney stones
Conditions of the reproductive organs giving rise to pain
include endometriosis, pelvic inflammatory disease, ovarian cysts, fibroids.
If you hav ealready consulted a Gynaecologist and any abnormality is ruled out, then it most probably is due to the kidney stones.
You can take the medications that have been prescribed for the pain.