I have the same problem with my 4 year old who is very hygienic in every sense of the word. I just found this website which is very useful. Please take a look.
http://www.netdoctor.co.uk/ate/childrenshealth/200572.html
my 3 year old had bad smell under arms it was yeast infection dr said it is wear her under arms dont get air i dont now if this helps or not
Did you ever find anything out about how to control your daughters smelly underarms? My son is almost 2 and has had very stinky, smelly armpits for about 6 months or so now. He has some health issues and is on many medications (he just had a kidney/liver transplant). I have asked his pediatrician, his tx doctors, and his endocrinologist about this and everyone is at a loss. They say that sometimes babies go through some kind of early puberty but they don't believe this is his case. Any ideas?
Although I am not a doctor, I am a Mother. I would recommend seeing a Pediatirc Endocrinologist!