I don't think anyone has a complex necessarily, just two different styles. Some people don't like "visual descriptions" (color, weight, size) 'labeling' their babies. She seems to be in that category since she didn't like nicknames for her first, and she mentions possible complexes. She's "particular and sensitive" but that's her right. She did make sure to let you know she wasn't upset, so she asserted herself politely. It probably did bug her when you called her baby chocolate chip the first day too, she just thought it would pass on it's own. And I don't think she was MAD, or thinks you meant anything NEGATIVE, she just doesn't like it, and YES, pregnancy hormones...So, yeah, you're kind of on eggshells, but it's a pretty easy request to follow if you value her friendship.
If I was you, I'd just be nice and say, "OK, I totally understand, I really had no idea it was offensive". Which she already knows, which is why she specified she wasn't upset. Just because she doesn't want her child called chocolate chip doesn't mean she thinks the baby's skin color isn't beautiful. If one of my friends called one of my kids "White Chocolate Square" a few times it might strike me as odd that it calls attention to their skin color for no reason, but I wouldn't be mad or anything. But it would bug me.
Speaking of "chocolate skin", my ex told me when he was a very small kid and lived in a white neighborhood, he saw a black person and said, "Oooh, look, a chocolate man!" and really embarrassed his parents. Hopefully the man was nice like you and didn't mind :)
If you like your friend, allow her to be picky.