My dd had blood in her stool as well when she was younger, 3 doctors told us it was fissures as well but when it continued we found out it was milk protein allergy. How much blood is there? My first thought is the allergy. My dd would get blood if I ate ANY amount of trace dairy. In the beginning I had eliminated what I thought was all dairy, then had oatmeal (the type you add hot water to) and she had blood, turns out I couldn't eat ANYTHING made with any amount of dairy whatsoever.
Make sure your doctor doesn't bother with the allergy skin prick test, it doesn't often show as positive for the protein allergy. You have to get blood work done, then they do a milk challenge, then blood work again to check levels (of...I can't remember what).