Being bigger does result in larger breasts, and because more percentage will be fat they are likely to be less perky = nipple lower.
Hope this isn't too late to help!!!
I definitely agree with "Diphie" above. The problem is that there is no real problem beyond the fact that your sweet girlfriend has bought into the IMAGE of what is beautiful. She really has to listen to YOU and how you feel about her breasts and nipples. A reasonable man will find beauty, sexual attractiveness and excitement wherever he FEELS it, not because he is told it must be a certain way, or with a certain type of body part. This may sound stupid and chauvinistic, but just think, it's like being with two different women at once! Two differently structured breasts and two differently styled nipples to play with and suckle, both on one beautiful woman! How fortunate you are!
Seriously, if her nipples and breasts respond to your touch, if they give her wonderful sensations, who cares where they are? They could be under her arms or on her backside for all it would matter. I know that YOU know that the only problem is in her head. If it really becomes an issue of self-image or self-confidence, at best she might consider seeing a therapist for her body image issues -- at worst, there is always plastic surgery to "even them out".
In any event, keep reassuring her that she is more beautiful than she knows, keep touching her in a loving way, keep enjoying her nipples (and everything else she has), and keep cumming for her in response to those magnificent breasts of hers. That's probably the greatest indicator of her sexual power, showing her that there's nothing wrong with her very special, very sexy body.