Hey, girls, and guys for that matter, can get turned off by something minor and just move their affections somewhere else. Could it have been your body? Maybe. But just as likely something else.
Keep on working out and getting in better shape, but I wouldn't lose too much sleep over why her interest got re-directed. It just happens sometimes. I had a movie watching first date (at her place) with a really hot chick one time. It was perfect, until I actually looked around at her kitchen, bathroom etc., and just noticed how dirty she was in general, and she was a professional, well put together woman.
There was something about it that just kind of turned me off on getting to know her more...and I'm by no means a picky, clean freak. She probably never knew the real reason why I never hooked back up with her, because I just told her I was busy and we stopped talking.
Maybe she hit the gym harder after that, who knows? See what I mean