If everything is really the same than it's obviously the geometry. Only your LBS can explain. Are you positive both framesets are the same model from the same year? I don't follow the pista too closely but they seem to look quite similar from year to year.
I do have a question though:
today I stopped in a track stand for a sec at an intersection and caught my toe, which is how I noticed the problem....I guess I can be super careful making sharp turns and not trackstand ever
Why are you hitting your toe on a trackstand? That's either not toe overlap or you're doing it wrong.