Since you state she's had this itching between her butt cheeks in her cleft for the past two years--right around the time she would have started eating table foods and cereal on a daily basis--I would have her tested for Celiac Disease. She might not actually have Celiac disease; she might have Gluten Intolerance. Either way, itching skin manifestations (to include that area; I know, I have it, along with hemmorhoids, fissues, etc.) usually tend to point to a food culprit.
Does she have diarrhea, constipation, or alternating diarrhea and constipation? Does she have other skin rashes or break out in different areas of her body? Losing hair? Canker sores in the mouth? Slow growth, short for her age, seems to always eat but doesn't gain (i.e., is skinny as a stick)? Does her tummy hurt, or is it bloated/distended, with maybe rumbling sounds? Does she pass a lot of gas? Does she get colds or infections easily, then have a hard time getting rid of them? Does she crave carbohydrates (bread, pasta) and/or sweets? Does she like or hate meat (protein)? Does she vomit after eating? Have a lot of tummyaches? All of these questions could point toward gluten intolerance/sensitivity, celiac disease, or other food intolerances.
Break outs on the skin are one of the biggest tip offs that something going into the body isn't liked by the body. If her Pediatrician won't do anything to find the problem, I'd seriously take her to see an Integration Doctor (an alternative medicine doctor who holds a medical degree but straddles the line between conventional medicine and alternative/homeopathic medicine). I had to break down and take both myself and my daughter to see an Integration medicine doctor. Right now, we're still testing. However, she's found so many problems already, she's already earned her sainthood, in my book. ;)
Keep us posted.