I didn't read all responses but make sure she is wiping front to back and that she is cleaning herself "back there" really good. She may be wiping too hard, causing an irritation. If the doctor can't find anything and you have tried the above, take her to another doctor, perhaps a "pediatric gynocologist".
You could try body wash that is made for sensitive skin and perhaps fragrance free--like Aveeno.
Of course--make sure that she is not being physically harmed by anyone--that should be clearly obvious.
You could have her describe the pain: sharp, dull, itching, intermittent, when does it hurt, when does it not hurt, is it more external--not internal, is it towards her behind or more in the front.
Is her mom in the picture or any female like grandma??
Also, I when/if my kids have messy BM's, I help them clean themselves with a washcloth in clean water as opposed to the chemically wipes. If I use a wipe, I rinse it "with water" first to get the chemicals out.
She shouldn't be having any pain or irritation. We know that isn't normal.