heh, rachel i completely understand why somebody [you, in this case, along with others probably] would feel odd at the phrase. I refer to myself as a girl, still, it just doesn't feel right calling myself a 'woman' what with my age and all--i just don't feel like a woman yet, even though anatomically it's all there *smiles*. Still, though, the connotations that come with the phrase 'good girl' make me feel extremely good about myself. It is a nice reward for me, i must admit.
As stated in a previous post it's the phrase you're likely to say when talking to a child or a pet--it gives me the same feeling i hope my dog has when i tell her 'good girl!'. *giggles*