My friend got called that and since neither of us are American, it just sounded offensive to us.
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As an American, I honestly wouldn't know how to take it either.
OTOH, diner waitresses are kind of a special breed. Where most places the server tries to be part of the background, in a diner often the server is expected to be very personal. While most restaurants try to give a pleasant homogenous experience, in a diner one can expect to get a lot more local cultural flair. If there's a local accent or attitude, a diner waitress will often be playing it up to the extreme. For instance, people of both genders often get called things like "sweetie" or "honey", which is actually kind of condescending. They are expected to be snarky and have an attitude. There are even some places where part of the draw is how rude they are to you.
So it could be some localish quirk she was playing up. Something that a non-American might not have thought twice about. For instance, perhaps you had what sounded to her like a disagreement over the size or person to provide the tip, and the person who paid it seemed to have lost. In that case, it might have been intended as a crack about the treatment the "good girl" received from his dining partner. Its tough to say without being there.