S.H.
Is it perhaps something she does as a 'self-soothing' thing?
What is her behavior when she is scratching/rubbing her head?
Is it 'angry', 'frustrated', or is she just enjoying doing it?
Or is it only when she is tired? There may be your answer as to why she does it.
Also, if you are washing her hair everyday, at each bath... try to just wash her hair less frequently. Doctor's say that you don't have to wash the hair everyday....it's too drying. Especially for baby skin, which is more sensitive.
It's good that you don't see anything on her scalp be it sores, dandruff or lice.
Good luck...babies do all kinds of things, that don't always make sense to us. But at least, it does not seem to be 'harming' her or getting her scalp all scratched up.
Good luck in finding the reason,
Susan