Yeah, I have the same problem. I told a dealer when the car went in for the MFT update. When I picked up the car, he said Ford corporates' take is to wait 3k-4k miles before they'll take it very seriously. How you drove your car during break-in should have no noticeable impact, but I have noticed a few things.
Short trips on a cold engine will net me much lower mileage, and city mileage is fairly low to begin with. Short 5 mile trips after the car has sat for at least a few hours, I will only get around 23-24 MPG when driving so miserly, it makes me miserable. Drive normally, and I'm lucky to see 20mpg. The car really shines at cruising around 50-60mph, and I've noticed close to 40mpg in the stretches. You really need long stretches in a warm engine between lights when city driving to get anywhere near the city rated mileage. As a short trip, errand runner, this car would completely suck.
While this should be true for most cars, it is amplified in the Focus, from my experience. My 300hp/300 torques 535i when driven in a similar manner only gets about 2mpg less in the city. On the freeway, the Focus wipes the floor with it, though. Oh well, at least it uses regular.
I still plan to take it in again a little later, but I don't think it help. It could also be the larger PS3 tires on the Ti/ handling.