the effective top tube is longer on your new bike - and especially since you get comfortable when you straighten your elbows, I'd think that it might be a bit too long for you. You may be able to put a shorter stem on it, but definitely get a good fit on the whole bike. It sounds like its not properly set up for you anywhere...
both bikes are "43cm" bikes, but the only thing that measures is seat tube, so I'm thinking your sales person just gave you the size you had without taking into consideration that the Giant has a more compact geometry compared to your Trek. A w2xs may have been a better fit for you, but is still longer than your current bike. If you can still trade it in, maybe think aobut talking to someone more knowledgeable about fit to make sure you have the proper size and trade it for a smaller one if you don't.
*edit* - you may not be able to get a smaller size.... looks like the 2xs is only available in the OCR3 - humph, it always annoys me that they don't think small people might want a high end bike



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