I think that there would be some bright, red blood if there was a fissure .....

Have you thought about pin-worms?? This is VERY common in kids, especially if they play outside in the dirt and/or put their fingers in or near their mouths. I know that this can cause intense itching, and - because kids scratch! - can cause irritation in both the vaginal and rectal areas, which could cause pain. My daughter had a problem with this when she was about 4 ( I THINK she picked it up at her pre-school "sand & water table"! ... yuck!); it is easily taken care of with some over the counter (here in Canada, anyway) oral medication.

Hope you find the problem soon!