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Have they done a CT scan of your abdomen or ultrasound of your kidneys?
OK, one possibility is that you may be having reflux of urine up to the kidneys when you are urinating. This can cause pain. In order to evaluate for this, your doctor can do a test called a voiding cystourethrogram to see if there's reflux. There are Minor endoscopic procedures that can be done to prevent this reflux if this is what you have. Hope this helps.