why is there still blood and mucus

My three month old has had blood in her stools since day one.  They sent her to Children's Hospital, where they did multiple x-ray's and upon examination found that she had three anal fissures, probably caused by a forceful bowel movement.  Then, while she was still at the hospital they started detecting blood in her stools, but was not visible to the naked eye. I was breastfeeding, but they made me stop because her hemoglobin levels were also low, and they put her on a hyperallerginic formula that she is still on today.  Although her blood is normal now,and her white blood count is negative, she is STILL having mucusy stools with specks of blood, sometimes the mucus has blood in it.  She's had a colonoscopy already, and there was nothing too alarming, just inflamation (inflammation).  She's gaining weight like crazy, and generally seems very happy.  Why is her poop still like it is?   Can someone please give me an answer!?