When you're riding, relaxed as you can be, and you look down, do your handlebars (the flat, top part) mask the front hub, or is the front hub in front of or behind the top of the bars?

This is a little rule of thumb, and is not exact, but generally you want the front hub to be about masked by the handlebars when you are looking down. A little variation either way is probably okay, but alot...that could tell you that your top tube is too long (or too short, depending on if the hub is visible behind or in front of the bars). If the top tube is simply too long for you, you could try a shorter stem and/or push your seat forward (but you also want to make sure there is a straight line down from kneecap to pedal axle). They should have measured this with a pendulum when you got the pro fit.

Best to try this on a trainer, by the way (with the front wheel elevated so the top tube is level--use a phone book or two under the front wheel and a spirit level).

EDIT, I'm 5'6 with long legs. I've only recently had the EUREKA bike, after years of racing and riding and being uncomfortable on, it turns out, too-big bikes. My new road bike is 49cm, which most people would say is way too small for me. But it works wonders! Everyone is proportioned differently; you'll get the right combo eventually.