Maybe the relationship was progressing at a normal, comfortable level and you sort of dropped a 'do or die' bomb on her - almost sounds like you gave her some sort of weird ultimatum about how she can act *IF* she really means it.
Well, part of the process of falling for someone IS sharing those special looks and the allowance of the occasional gentle, no-pressure show of affection. These can occur quite comfortably and naturally when you are getting to know someone and are nice because you can retain a safe platform for continuing to get to know them on a flirty friendship level before you are serious enough ('actually dating') and have to worry about it going any further physically or emotionally.
She was probably a bit put off by the abruptness and (for lack of a better description) 'demanding neediness' you displayed by suddenly forcing it to another level permaturely. That she came back in and stayed seems like an indication she does enjoy your company, etc and more than likely has been thinking of you romantically. But maybe you might want to dump some of those sore feelings you have left over from your previous relationship before jumping into this new one. I know there have been times when a guy moved way quicker than what I was intending and it really became a turn off because there was an air of DESPERATION to it - like "I am wounded so you need to prove to me you are not going to hurt me, too" by somehow showing him a loyalty that maybe he (or you) have not quite actually EARNED, yet...
..simply because the relationship has not had the time to grow that much.
Doesn't sound like it harmed anything, and now she knows how you feel - nothing wrong with letting someone know you care about them. I mainly would warn against taking old feelings into the new relationship....like because of how the other girl treated you this new one has to prove herself to you, etc. Be particularly careful of overreacting to things if you are still seeing them through the betrayal/actions of the other.
Good luck! =)