Since the doc already looked and didn't see anything obviously concerning, it sounds like it may very well be one of the PPs ideas: soap, self-exploration, some other irritant.
But I just wanted to chime in on one of the first PPs including abuse in the list even though it's unlikely. OP you said it wasn't possible because she's not alone with anyone long enough for that to be an issue. And I have no reason to doubt that that's true, but it still feels important to ask you if you asked her simply whether anyone else touches here there or not or whether anyone has hurt her there and see what she says.
I totally get not wanting to be alarmist, and not wanting to freak yourself or dd out. And maybe you did already ask her that and you just didn't say so here. But the fact that you don't think she's alone with anyone else long enough for that to be in an issue does not remove the fact that in this kind of case, especially when so far you haven't identified exactly what the problem is, it is *always* a good idea to ask (in a non-alarmist, kinda light way - but in a clear way) "Honey, does anyone ever touch you there?" and just see what she says. If she says no and doesn't seem in any way troubled by you asking, cool, move on, cross that off the list because now you've asked and she's been calm and fine about her answer.
But as someone who works for CPS, I have to say that sometimes when child abuse is confirmed, there is a parent or family member who swore up and down that it was impossible. And sometimes it really, truly is their impression that there wasn't the opportunity, but in the end they were wrong about that. So I guess I want to explain why even though you feel it's impossible, it's still worth checking on at least a little since so far no other definite cause for her pain has been confirmed yet.
Based on the doc saying they didn't see anything concerning, sounds most likely that this isn't the issue (sometimes there is physical evidence of abuse, some times there isn't). But it made me nervous that you may not have asked your dd about it in any way to make sure she didn't seem upset or troubled when that idea is brought up.
By the way, for those worried about upsetting your dd, most younger kids who are not being abused will either not even regoster the question (if asked in a non-anxious, non-alarmist way) or just find it curious. And older kids you can obviously explain why you're asking and that you don't want to freak them out, but you also want to remind them that they can and should tell you if ever anyone is doing something to them that they don't want or are afraid to tell you about.
Hope you find the cause soon and that it's as easy as changing soaps or changing the kind of undies she wears.
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