I wonder as well if this is at least a fitting issue, it sounds like you are too scrunched up on the bike. I am 5'3 myself and ride a 48 cm - but I've a short reach and require a very upright riding position - if it weren't for those things I would ride the next size up.

Did your LBS do a full fitting for you (lots of measurements, checking you out on the bike which was probably on a trainer of some sort, making adjustments to the fit), or was it something quicker than that? Do you know what your inseam is?